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A Unified Environment for the

Development and Performance Tuning
of Parallel Scientific Applications
Jay Alameda, NCSA
jalameda@ncsa.uiuc.edu
Wyatt Spear, U. Oregon

wspear@cs.uoregon.edu
Galen Arnold, NCSA

arnoldg@ncsa.uiuc.edu
April 4-5, 2013

Portions of this material are supported by or based upon work supported by the Defense
Advanced Research Projects Agency (DARPA) under its Agreement No. HR0011-07-9-0002, the
United States Department of Energy under Contract No. DE-FG02-06ER25752 and the SI2-SSI
Productive and Accessible Development Workbench for HPC Applications, which is supported by
the National Science Foundation under award number OCI 1047956
Tutorial Outline
Time (Tentative!)
Module
Topics
Presenter
10:30-11:00
1. Eclipse and PTP

Installation
Installation of Eclipse and PTP

(can start early as people arrive)
Jay
11:00-11:30
2. Introduction & Overview
Eclipse architecture & organization overview
Wyatt
11:30-12:00
3. Developing with Eclipse
Eclipse basics; Creating a new project from CVS;

Local, remote, and synchronized projects
Jay
12:00-1:00
Lunch
1:00-2:30
3. Developing with Eclipse

(continued)
Continue from before the break

Editing C files; MPI Features; Building w/Makefile
Resource Managers and launching a parallel app
Fortran, Refactoring, other Advanced Features
Wyatt
2:30-3:00
4. Debugging Part A
Debugging an MPI program
Jay
3:00-3:30
Break
3:30-4:00
4. Debugging Part B
Debugging an MPI program
Jay
4:00-5:00
5a. Performance Tuning &

Analysis Tools
1. TAU (Tuning and Analysis Utilities)

ETFw (External Tools Framework)
Wyatt
Tutorial Outline
Time (Tentative!)
Module
Topics
Presenter
8:30-9:30
5b. Performance Tuning &

Analysis Tools
2. Other tool integration with PTP
Wyatt/Jay
9:30-10:00
6. Developing WRF with

Eclipse
Overview of how to work with WRF from Eclipse
Jay
10:00-10:30
Break
10:30-11:30
6. Developing WRF with

Eclipse
Overview of how to work with WRF from Eclipse
Jay
11:30-12:00
7. Other Tools, Wrapup
Other Tools, website, mailing lists, future features
Jay
12:00-1:00
Lunch
1:00-3:00
Bring your own

code/Advanced TAU
3:00-3:30
Break
3:00-5:00
Bring your own

code/Advanced TAU
Wyatt/Jay
Wyatt/Jay
PTP Tutorial Slide Topics
PDF
page #
Slide page
# prefix
PTP Installation
Install-
PTP Introduction
21
Intro-
Eclipse Basics
30
Basic-
Adding a remote shell in Eclipse
43
Shell-
Creating a Synchronized project from existing remote dir (Project creation alt. #1)
51
Sync-
Creating a project from CVS Team features then convert to Synchronized project
(Project creation alt. #2) for SC tutorial we will do #2
73
CVS-
Eclipse Editor Features
93
Editor-
MPI Programming Features (similar features for OpenMP, UPC, OpenSHMEM, OpenACC)
110
MPI-
Using SSH tunnelling
132
Tunnel-
Building a Project on a remote target
135
Build-
Running an Application on remote target
153
Run-
Fortran
174
Fortran-
Search and Refactoring: Advanced Features
191
Advanced-
NCSA/XSEDE Features: GSI Authentication, MyProxy Login, etc
208
NCSA-
Parallel Debugging
215
Debug-
Performance Tools introduction
250
Perf-
Performance Tools TAU (Tuning and Analysis Utilities)
253
TAU-
Performance Tools GEM (Graphical Explorer of MPI Programs)
272
GEM-
Performance Tools Linuxtools gcov/gprof in Eclipse
308
Linux-
Wrap-up
328
WrapUP-
Final Slides, Installation

Instructions
Please go to
http://wiki.eclipse.org/PTP/tutorial
s/SEA2013 for slides and
installation instructions
Installation
Objective
To learn how to install Eclipse and PTP
Contents
System Prerequisites
Eclipse Download and Installation of Eclipse for
Parallel Application Developers
Installation Confirmation
Updating the PTP within your Eclipse to the latest
release
Installation
Install-0
System Prerequisites
Local system (running Eclipse)
Linux (just about any version)
MacOSX (10.5 Leopard or higher)
Windows (XP on)
Java: Eclipse requires Sun or IBM Java

Only need Java runtime environment (JRE)
Java 1.6 or higher
Java 1.6 is the same as JRE 6.0
The GNU Java Compiler (GCJ), which comes
standard on Linux, will not work!
OpenJDK, distributed with some Linux distributions,
has not been tested by us but should work.
See http://wiki.eclipse.org/PTP/installjava
Installation
Install-1
Eclipse Packages
The current version of Eclipse (4.2) is also
known as Juno
Eclipse is available in a number of different
packages for different kinds of development
http://eclipse.org/downloads
For PTP, we recommend the all-in-one

download:
Eclipse for Parallel Application Developers
We often call this the Parallel Package
Installation
Install-2
Exercise
1. Download the Eclipse for Parallel Application
Developers package to your laptop
Your tutorial instructions will provide the location of
the package
Make sure you match the architecture with that of
your laptop
2. If your machine is Linux or Mac OS X, untar

the file
On Mac OS X you can just double-click in the Finder
3. If your machine is Windows, unzip the file

4. This creates an eclipse folder containing the
executable as well as other support files and
folders
Installation
Install-3
Starting Eclipse
Linux
From a terminal window, enter
<eclipse_installation_path>/eclipse/eclipse &
Mac OS X
From finder, open the eclipse folder where you installed
Double-click on the Eclipse application
Or from a terminal window
Windows
Open the eclipse folder
Double-click on the eclipse executable
Installation
Install-4
Specifying A Workspace
Eclipse prompts for a workspace location at
startup time
The workspace contains all user-defined data
Projects and resources such as folders and files
The default workspace location is fine for this tutorial
The prompt can be
turned off
Installation
Install-5
Eclipse Welcome Page

Displayed when Eclipse is run for the first time
Select Go to the workbench
Install-6
Installation
Checking for PTP Updates

From time-to-time there may be newer PTP
releases than the Juno release
Juno and Parallel package updates are released only in
September and February
PTP maintains its own update site with the most

recent release
Bug fix releases can be more frequent than base Eclipse
(e.g. Juno), and what is within the parallel package
You must enable (and install from) the PTPspecific update site before the updates will be
found
SEA Note: we will show you specific instructions
on applying a needed update on slide 9
Installation
Install-7
Updating PTP
Now select Help>Install New Software
In the Work With: dropdown box, select this update site,
or enter it:
http://download.eclipse.org/tools/ptp/updates/juno
Installation
Install-8
Updating PTP: SEA

Now select Help>Install New Software
Next to Work With: dropdown box, select Add
Installation
Install-9
Updating PTP: SEA (2)

Label the nightly
build site, add
location
http://download.eclipse.org/too
ls/ptp/builds/juno/nightly
Installation
Install-10
Updating PTP (2)

Easiest option is to check everything - which updates
existing features and adds a few more
Note: for our tutorial, this installs extra features youll

need later anyway (GEM, TAU)
Select Next to continue updating PTP
Select Next to confirm features to install
Installation
Install-11
Updating PTP (3)

Accept the License agreement and select Finish
Dont restart Eclipse yet!

see next slide (for one more update) before accepting to restart
Eclipse
or you can restart eclipse and do it then
Installation
Install-12
Updating PTP CDT fix

Currently CDT (C/C++ Development Tools) needs a fix
for remote includes
Well install from another update site to fix this:
In the Work With: dropdown box, add:
http://download.eclipse.org/tools/ptp/updates/juno/cdt
Select All
Next, Next, accept license,
Finish to complete the
install
Installation
Install-13
Updating PTP - restart

Select Yes when prompted to restart Eclipse
Installation
Install-14
Updating Individual Features

Its also possible (but a bit tedious) to update features
without adding any new features
Open each feature and check the ones you want to update
Icons indicate: Grey plug: already installed

Double arrow: can be updated
Color plug: Not installed yet
Note: if network is slow, consider unchecking:
Installation
Install-15
Restart after Install

If any new top-level features
are installed, they will be
shown on the welcome screen
We only updated PTP, so we
land back at C/C++
Perspective
Help>About or Eclipse > About Eclipse

will indicate the release of PTP installed
Further Help>Check for Updates will find future updates on
the PTP Update site
Installation
Install-16
Exercise
1. Launch Eclipse and select the default
workspace
2. Configure Eclipse to check for PTP updates
3. Update all PTP features to the latest level
4. Install the optional features of PTP, including
TAU and GEM
Selecting all features accomplishes 3. and 4.
5. Install the CDT fix

6. Restart Eclipse once the installation is
completed
Installation
Install-17
Introduction
Objective
To introduce the Eclipse platform and PTP
Contents
New and Improved Features
What is Eclipse?
What is PTP?
Introduction
Intro-0
What is Eclipse?
A vendor-neutral open-source workbench for
multi-language development
A extensible platform for tool integration
Plug-in based framework to create, integrate
and utilize software tools
Introduction
Intro-1
Eclipse Features
Full development lifecycle support
Revision control integration (CVS, SVN, Git)
Project dependency management
Incremental building
Content assistance
Context sensitive help
Language sensitive searching
Multi-language support
Debugging
Introduction
Intro-2
Parallel Tools Platform (PTP)

The Parallel Tools Platform aims to provide a highly
integrated environment specifically designed for parallel
application development
Features include:
An integrated development environment (IDE) that
supports a wide range of parallel architectures and runtime
systems
A scalable parallel debugger
Parallel programming tools
(MPI, OpenMP, UPC, etc.)
Support for the integration
of parallel tools
An environment that simplifies the
end-user interaction with parallel systems
http://www.eclipse.org/ptp
Introduction
Intro-3
Eclipse PTP Family of Tools

Coding & Analysis
Launching &
Monitoring
(C, C++, Fortran)
Introduction
Performance Tuning
Parallel Debugging
(TAU, PPW, )
Intro-4
How Eclipse is Used

Editing/Compiling
Local Source
Code
Introduction
Remote
Source Code
Intro-5
How Eclipse is Used

Launching/Monitoring
Source Code
Executable
Introduction
Intro-6
How Eclipse is Used

Debugging
Source Code
Executable
Introduction
Intro-7
How Eclipse is Used

Performance Tuning
Source Code
Executable
Perf. Data
Introduction
Intro-8
Eclipse Basics
Objective
Learn about basic Eclipse workbench concepts:
projects,
Learn about projects: local, synchronized, remote
Contents
Workbench components: Perspectives, Views, Editors
Local, remote, and synchronized projects
Learn how to create and manage a C project
Learn about Eclipse editing features
Eclipse Basics
Basic-0
Eclipse Basics
A workbench contains the menus, toolbars, editors and
views that make up the main Eclipse window
The workbench represents
the desktop development
environment
Contains a set of tools
for resource mgmt
Provides a common way
of navigating through
the resources
Multiple workbenches
can be opened at the
same time
Only one workbench can
be open on a workspace
at a time
Eclipse Basics
view
view
editor
view
perspective
Basic-1
Perspectives
Perspectives define the layout of views and
editors in the workbench
They are task oriented, i.e. they contain
specific views for doing certain tasks:
C/C++ Perspective for manipulating compiled code
Debug Perspective for debugging applications
System Monitoring Perspective for monitoring
jobs
You can easily switch between perspectives

If you are on the Welcome screen now, select
Go to Workbench now
Eclipse Basics
Basic-2
Switching Perspectives
Three ways of changing
perspectives
1. Choose the Window>Open
Perspective menu option
Then choose Other
2. Click on the Open Perspective button in the
upper right corner of
screen (hover over it to
see names)
3. Click on a
perspective
shortcut button
Eclipse Basics
Basic-3
Which Perspective?
The current perspective is displayed in the title
bar
Eclipse Basics
Basic-4
Views
The workbench window is
divided up into Views
The main purpose of a view is:
view
view
view
To provide alternative ways of presenting information

For navigation
For editing and modifying information
Views can have their own menus and toolbars

Items available in menus and toolbars are
available only in that view
Menu actions only
apply to the view
Views can be resized

Eclipse Basics
Basic-5
Stacked Views
Stacked views appear as tabs
Selecting a tab brings that view to the
foreground
Eclipse Basics
Basic-6
Expand a View
Double-click on a view/editors tab to fill the
workbench with its content;
Repeat to return to original size
Double
click
Double
click
Window > Reset Perspective

returns everything to original positions
Eclipse Basics
Basic-7
Help
To access help
Help>Help Contents
Help>Search
Help>Dynamic Help
Help Contents provides

detailed help on different
Eclipse features in a
browser
Search allows you to
search for help locally, or
using Google or the Eclipse
web site
Dynamic Help shows help
related to the current
context (perspective, view,
etc.)
Eclipse Basics
Basic-8
Eclipse Preferences
Eclipse Preferences allow
customization of almost
everything
To open use
Mac: Eclipse>Preferences
Others:
Window>Preferences
The C/C++ preferences

allow many options to be
altered
In this example you can
adjust what happens in
the editor as you type.
Eclipse Basics
Basic-9
Preferences Example
More C/C++ preferences:
In this example the
Code Style preferences
are shown
These allow code to be

automatically
formatted in different
ways
Eclipse Basics
Basic-10
Exercise
1. Change to a different perspective
2. Experiment with moving and resizing views
Move a view from a stack to beside another view
Expand a view to maximize it; return to original size
3.
4.
5.
6.
7.
Save the perspective

Reset the perspective
Open Eclipse preferences
Search for Launching
Make sure the Build (if required) before
launching setting is disabled
Eclipse Basics
Basic-11
Optional Exercise
Best performed after learning about projects, CVS, and editors
1.
Use source code formatting to format a source file, or a region

of a source file
Use Source>Format menu
2. In Eclipse Preferences, change the C/C++ source code style
formatter, e.g.
Change the indentation from 4 to 6
Make line wrapping not take effect until a line has a
maximum line width of 120, instead of the default 80
Save a (new) profile with these settings
Format a source file with these settings
3. Revert the file back to the original experiment with
Replace with HEAD, replace with previous from local history,
or reformat using original style
Eclipse Basics
Basic-12
Adding a Remote Shell

Objective
Learn how to add an additional Eclipse View with a shell
to a remote system
Learn how to do command line interaction with the
remote system right from Eclipse
Contents
Set up Remote Systems Explorer (RSE) connection
Add Remote Shell view
Connect to remote system
Allow opportunity to inspect remote system, copy file,
etc as needed
Eclipse Basics
Shell-0
Add the Remote Systems View

Open the Remote Systems view
Open it via Window>Show View>Other
Under Remote Systems, select
Remote Systems
Or it can be found in the
Remote C/C++ perspective
Probably gets added at the

bottom
Shell in a View
Shell-1
Define a new RSE connection

Select the Remote Systems view
Define a new connection
(buttons may be on the far
right side of the toolbar)
In the New Connection dialog,

Select SSH Only
Then Next
Shell in a View
Shell-2
Define a new RSE connection (2)

Add systems host info
Then Finish
Right click on Ssh

terminals, under your
new connection
Select Launch Terminal
Shell in a View
Shell-3
Define a new RSE connection (3)

Add your userid and
password
Click through any RSA
messages
And now you have a
terminal to the remote
system
Shell in a View
Shell-4
Notes
Why did we do this?
To show you can gain traditional access to a
remote host through Eclipse
Why did I have to specify the connection
information again?
Note: RSE Connection information is not
shared with PTP Synchronized projects.
PTP will allow using existing connections with
terminal consoles in a future release.
Shell in a View
Shell-5
RSE Connection Properties

To alter the properties e.g.
of the remote Terminal,
such as the userid used for
the login
Open/select the Remote
Systems view
Expand your connection
Right mouse on Ssh
Terminals and select
Properties
In Properties dialog,
select Subsystem
Eclipse Basics
Basic-6
Exercise
1. Add the Remote Systems view to your
workbench
2. Connect to the remote machine and open an
ssh terminal
3. Inspect home directory
Eclipse Basics
Shell-7
Creating a Synchronized Project

Objective
Learn how to create and use synchronized projects
Learn how to create a sync project directly from source
that already exists on a remote machine
Contents
Eclipse project types
Creating a synchronized project
Using synchronize filters
Converting an existing project to synchronized
Project Creation Alternative #1
In this scenario, we will use code existing on a remote host, and

create a synchronized project which copies it to the local machine
(Project Creation Alternative #1 is to check out code from a CVS
source code repository and then convert to a Sync project)
Synchronized Projects
Sync-0
Project Types
Local
Source is located on local machine, builds happen
locally
Remote
Source is located on remote machine(s), build and
launch takes place on remote machine(s)
Synchronized
Source is local, then synchronized with remote
machine(s) (or vice-versa)
Building and launching happens remotely
(can also happen locally)
Sync-1
Remote Projects
Projects types can be:
LaunchService
Compute
DebugService
BuildService
Executable
IndexService
FileService
Sourcecode
Local
Remote
Sync-2
-2
Projects types can be:
LaunchService
Compute
DebugService
BuildService
Executable
IndexService
FileService
Edit
Search/Index
Navigation
Localsource
code
Synchronize
Local
Sourcecode
copy
Remote
Sync-3
-3
C, C++, and Fortran Projects

Build types
Makefile-based
Project contains its own makefile (or makefiles) for
building the application or other build command
Managed
Eclipse manages the build process, no makefile
required
Sync-4
-4
Create Project
This module creates a Synchronized project
from source code already existing on the
remote system
- or
The CVS module creates a Synchronized
project from a CVS source code repository
Synchronized
Projects
Sync-5
Source Code for project

Source code exists on remote target
Sync-6
Create Synchronized Project

In the Project Explorer, right click then choose
New>Synchronized C/C++ Project if your project is C/C++ only
New>Synchronized Fortran Project if your project contains Fortran

files
This adds a Fortran nature so you can access Fortran properties, etc.
Sync-7
New Synchronized Project Wizard

Enter the Project Name
E.g. shallow
The Local Directory specifies
where the local files are located
Leave as default
The Remote Directory specifies
where the remote files are located
Select a connection to the remote
machine, or click on New to create
a new one
(See next slide)
Browse for the directory on the
remote machine
Sync-8
Creating a Connection
In the Target Environment Configuration
dialog
Enter a Target name
for the remote host
Enter host name,
user name, and
user password or
other credentials
Select Finish
If your machine access requires
ssh access through a
frontend/intermediate node, use
localhost and port see
alternate instructions
Sync-9
Project Type & Toolchain

Choose the Project Type
If you are synchronizing with an

existing project, use Makefile
Project>Empty Project
Otherwise, choose the type of project
you want to create
Choose the toolchain for the remote

build
Use a toolchain that most closely

matches the remote system
Choose a toolchain for the local

build
This is used for advanced

editing/searching
Use Modify File Filtering if

required (see later slide)
Click Finish to create the project
Sync-10
Synchronized Project
Synchronized projects are indicated
with a synchronized icon
Right click on project to access
Synchronization menu
Select Auto-Sync to enable/disable
automatic syncing
Project Auto-Sync Settings are used
to determine which configurations are
synchronized (Active only, All or None)
Sync Active/All Now to manually
synchronize
Filter to manage synchronization
filters
Sync-11
Synchronize Filters
If not all files in the remote project should be
synchronized, a filter can be set up
For example, it may not be desirable to synchronize
binary files, or large data files
Filters can be created at the same time as the

project is created
Click on the Modify File Filtering button in the
New Project wizard
Filters can be added later

Right click on the project and select
Synchronization>Filter
Sync-12
Synchronize Filter Dialog

Files can be filtered individually
by selecting/unselecting them in
the File View
Include or exclude files based on
paths
Include or exclude files based on
regular expressions
Sync-13
Synchronized Project Properties

Synchronized project
properties can be configured
manually
Open the project properties,
then select C/C++
Build>Synchronize
Each configuration is
associated with a remote
connection and a root
directory
Can be changed manually,
but only if you know what
you are doing!
Sync-14
Changing Remote Connection Information

If you need to change remote connection
information (such as username or
password), use the Remote
Environments view
Stop the remote

connection first
Right-click and
select Edit
Note: Remote Host may be stopped
Any remote interaction starts it
No need to restart it explicitly
Sync-15
Converting a Local
C/C++/Fortran Project
to a
The following slides are for reference.
Our project is already a Synchronized Project.
Sync-16
Converting To Synchronized
If source files exist on the local machine and you wish to
convert it to a Synchronized Project on a remote
system
Select File>New>Other
Open the Remote folder
Select Convert C/C++
or Fortran Project to a
Click Next>
Sync-17
Convert Projects Wizard

Select checkbox next to shallow
Only C/C++/Fortran projects will be in the
list of candidates for conversion to Sync
project
For Connection:, click on New

Unless you already have a connection
The tutorial instructor will indicate

what to enter for:
Target name
Host name of remote system
User ID
Password
Click Finish to close it

The connection name will
appear in the
Convert Projects
wizard for Connection
Sync-18
Convert Projects Wizard (2)

Back in the Convert Projects dialog,
we specify where the remote files
will be stored
Enter a directory name in the
Remote Directory field:
select Browse
Sample: /u/ac/trainXX/shallow
Typing a new directory name creates it
This should normally be an empty directory
since local files will be copied there
Project files will be copied under this
directory
Click Finish
The project should synchronize
automatically
Sync-19
10
Exercise
1. Create a synchronized project
Your login information and source directory will be
provided by the tutorial instructor
2. Observe that the project files are copied to your

workspace
3. Open a file in an editor, add a comment, and
save the file
4. Observe that the file is synchronized when you
save the file
Watch lower-right status area; confirm on host system
Sync-20
Optional Exercise
1. Modify Sync filters to not bring the *.o files and
your executable back from the remote host
Rebuild and confirm the files dont get copied
Sync-21
11
Eclipse CVS Team Features

Objective
Learn how to use a source code repository with Eclipse
Learn how to create a Synchronized project
Contents
Checking out project in CVS
Setting up a Connection for a Synchronized Project
Handling changes; Comparing files (diffs)
Project Creation Alternative #2
In this scenario, we will check out code from a CVS source code
repository, setting it up as a synchronized project on a remote host.
(Project Creation Alternative #1 in this PTP tutorial is to create a
Synchronized project directly from code existing on a remote host)
CVS Source Code Repository
CVS-0
Importing a Project from CVS

Switch to CVS Repository
Exploring perspective
Window > Open Perspective > Other
Select CVS Repository Exploring
Select OK
Right click in CVS Repositories

view and select New>Repository
Location
CVS Source Code

Repository
CVS-1
Add CVS Repository

Enter Host: cvs.ncsa.uiuc.edu
Repository path:
/CVS/ptp-samples
For anonymous access:
User: anonymous
No password is required
Connection type: pserver (default)
For authorized access:

User: your userid
Password: your password
Connection type: change to extssh
Select Finish
CVS Source Code

Repository
CVS-2
Checking out the Project

Expand the repository location
Expand HEAD
Expand samples
Right click on shallow and select
Check Out As
On Check Out As dialog, select
Finish
The default of
Check out as a
project configured
using the New
Project Wizard is
what we want
CVS Source Code
Repository
CVS-3
New Project Wizard

As project is checked out from
CVS, the New Project Wizard
helps you configure the
Eclipse information to be
added to the project
Expand Remote
Select
Synchronized C/C++
Project
and click on Next>
CVS Source Code

Repository
CVS-4
New Project Wizard (2)

Enter shallow as project name
Under Project type, expand
Makefile project
- scroll to the bottom
Select Empty Project

For Remote Toolchain,
Select Linux GCC
In general, choose a toolchain that

matches the compiler you intend to
use on the remote system
For Local Toolchain

If you intend to build on the
local machine, select this; it
is optional
Next slide connection
CVS Source Code

Repository
CVS-5
Select Remote Connection:

UCAR SEA Workshop
For Connection:, click on New
Unless you already have a connection
Target Environment Configuration :
Target name: yellowstone

Host name of remote system
yellowstone.ucar.edu
User ID
Password: do not enter
Note: if you need to use ssh tunneling*,
use Localhost; the Advanced
button lets you enter the port #
Select Finish
CVS Source Code

Repository
* See http://wiki.eclipse.org/PTP/FAQ
and search for tunnel
Basic-6
Select Remote Directory

Back in the New
dialog, select the Browse
button under Remote
Directory
You will be asked for your
token response
This is the first time the

connection is used
For Project Location,
enter new directory name
(or select existing dir)
Hit OK, then Finish
CVS Source Code

Repository
Basic-7
Project successfully checked out

Switch to the C/C++ Perspective
when prompted after checking
out the code
You should now see the shallow project in your
workspace
Project is
synchronized
with remote
host
Expand the
project root
to see the
projects
contents
CVS Source Code

Repository
CVS-8
Synchronizing the Project

Because we will be running on a remote
system, we must also build on that system
Source files must be available to build
The synchronized project does this
Files are synchronized automatically when
they are saved
A full synchronize is also performed prior to a
build
CVS Source Code

Repository
CVS-9
Back in the Project
Explorer, decorator on
project icon indicates
synchronized project
Double-+ icon
C Project w/o Sync

CVS Source Code

Repository
CVS-10
Team Features
CVS Source Code

Repository
CVS-11
Team Features
Eclipse supports integration with multiple
version control systems (VCS)
CVS, SVN, Git, and others
Collectively known as Team services
Many features are common across VCS

Compare/merge
History
Check-in/check-out
Some differences
Version numbers
Branching
CVS Source Code
Repository
CVS-12
Two meanings for Synchronize

PTPs synchronize
Copy files in synchronized projects between local and
remote to mirror them
Team synchronize
Show differences between local project and source
code repository versions
CVS Source Code

Repository
Basic-13
CVS Features
Shows version numbers next to
each resource
Marks resources that have
changed
Can also change color (preference
option)
Context menu for Team

operations
Compare to latest, another
branch, or history
Synchronize* whole project (or
any selected resources)
CVS Source Code
Repository
* Team synchronize
CVS-14
How to tell that youve

changed something
Open calc.c
Add comment at line 40
Save file
File will be marked >
to indicate that it has
been modified
CVS Source Code

Repository
CVS-15
Comparing single file

with whats in the repository
Right-click on calc.c and
select Compare
With>Latest from HEAD
Even if you didnt create project
from CVS, you can try Compare
With>Local History
Compare editor will open

showing differences
between local (changed)
file and the original
Buttons allow changes to
be merged from right to
left
Can also navigate
between changes using
buttons
CVS Source Code
Repository
CVS-16
Comparing your project

with whats in the repository
Right-click on project
name (or any subset)
and select
Team>Synchronize
with Repository
Team Synchronizing
perspective will open
List of changed files
appears
Double-click on a file to
see the diff viewer
Buttons allow changes to
be merged from right to
left
Can also navigate
between changes using
buttons
CVS Source Code
Repository
CVS-17
Revert To The Latest Version

To replace your project contents to the current
contents of the project in the src code repo,
Right-click on the shallow project
and select Replace With>Latest from HEAD
Review the resources that will be replaced,

then click OK
CVS Source Code

Repository
CVS-18
Exercise
Check out the shallow project from CVS as a
synchronized project - as described in this
module
Optional Exercise
1. Name every person who modified the Makefile
2. Identify which parts of the Makefile changed
since revision 1.3
Hint: Right-click the Makefile and select Team > Show History.
Both of these can be done from the History view.
CVS Source Code Repository
CVS-19
10
Editor Features
Objective
Learn about Eclipse editor features
Contents
Saving
Editor markers
Setting up include paths
Code analysis
Content assistance and templates
Editor Features
Editor-0
Editors
An editor for a resource (e.g. a file) opens when you
double-click on a resource
The type of editor depends on the type of the resource
.c files are opened with the
C/C++ editor by default
You can use Open With to
use another editor
In this case the default
editor is fine (double-click)
Some editors do not just edit raw text
When an editor opens on a resource, it stays open across

different perspectives
An active editor contains menus and toolbars specific to that
editor
Editor Features
Editor-1
Saving File in Editor

When you change a file in the editor,
an asterisk on the editors title bar
indicates unsaved changes
Save the changes by using

Command/Ctrl-S or File>Save
Undo last change using Command/Ctrl Z
Editor Features
Editor-2
Editor and Outline View

Double-click on
source file
Editor will open in
main view
Outline view is
shown for file in
editor
Console shows
results of build,
local runs, etc.
Editor Features
Editor-3
Source Code Editors & Markers

A source code editor is a
special type of editor for
manipulating source
code
Language features are
highlighted
Marker bars for showing
Breakpoints
Errors/warnings
Task Tags, Bookmarks
Location bar for

navigating to interesting
features in the entire file
Icons:
Editor Features
Editor-4
Include Paths (1)
In order for editor and build features to work properly, Eclipse needs to know
where your include files are located
The build environment on the remote host knows your include files etc., but
we must tell Eclipse so that indexing, search, completion, etc. will know where
things are
Open Project Properties
Expand C/C++ General
Select Preprocessor
Include Paths
Click GNU C, then CDT
User Setting Entries,
then click Add
In upper right, select
Filesystem in pulldown
A UNC-style path specifies
//<connection>/<path>
Enter Path
//trestles/opt/openmpi/incl
ude
Select OK
Editor Features
Editor-5
Include Paths (2)

After adding include directory, it should
appear in the list
Bug: on Mac, it appears as blank. Close and re-open the twisty to see
the correct value.
Add second value:
//trestles/usr/include
... the same way
You should have

two entries:
Editor Features
Editor-6
Include Paths (3)

Select OK
The C/C++ Indexer should run
Lower right status area indicates it
If not force it via Project Properties>Index>Rebuild
Editor Features
Editor-7
Code Analysis (Codan)

If you see bug icons in the editor marker bar, they
are likely suggestions from Codan
If include files are set correctly, they should not appear.
Code checkers can flag possible errors, even if

code is technically correct
To turn them off, use Preferences
Window > Preferences or Mac: Eclipse > Preferences
C/C++ > Code Analysis
and uncheck
all problems
Select OK to
close
Preferences
Uncheck all
Editor Features
If icons dont disappear:

Right mouse on Project >
Run C/C++ Code Analysis
You can also enable/disable
this per project in Project
Properties
Editor-8
Line Numbers
Text editors can show line numbers in the
left column
To turn on line
numbering:
Right-mouse click in
the editor marker bar
(at editor left edge)
Click on Show Line
Numbers
Editor Features
Editor-9
Navigating to Other Files

On demand hyperlink
In main.c line 135:
Hold down Command/Ctrl key
e.g. on call to initialise
Click on initialise to navigate
to its definition in the header file
(Exact key combination
depends on your OS)
E.g. Command/Ctrl and click on
initialise
Open declaration
Right-click and select Open
Declaration will also open the
file in which the element is
declared
E.g. in main.c line 29 right-click
on decs.h and select Open
Declaration
Editor Features
Note: may need to left-click

before right-click works
Editor-10
Navigating to Remote Files

Note: remote includes must be set up
correctly for this to work
On demand hyperlink
In main.c line 73:
Ctrl-click on fprintf
stdio.h on remote system opens
Open declaration (or F3)

In main.c, right-click and select
Open Declaration e.g on <stdio.h>
File from remote system is opened.
Hover over editor name tab to see remote

location.
Editor Features
Editor-11
Content Assist & Templates

Type an incomplete function name e.g. get into the editor,
and hit ctrl-space
Select desired completion value with cursor or mouse
Code Templates: type

for and Ctrl-space
Editor Features
More info on code templates later
Hit ctrl-space again

for code templates
Editor-12
Hover Help
Hover the mouse over a program element in
the source file to see additional information
Editor Features
Editor-13
Inactive code
Inactive code will appear grayed out in the
CDT editor
Editor Features
Editor-14
Exercise
1. Open an editor by double clicking on a source file in the
Project Explorer
2. Use the Outline View to navigate to a different line in
the editor
3. Back in main.c, turn on line numbering
4. In main.c, ctrl-click on line 99, master_packet, should
navigate to its definition in the file
5. In worker.c, line 132, hover over variable p to see info
Editor Features
Editor-15
Optional Exercise
1. Type for, then activate content assist
Select the for loop with temporary variable template, insert it,
then modify the template variable
Surround the code you just inserted with #if 0 and #endif and
observe that it is marked as inactive
Save the file
2. What do these keys do in the editor?

Ctrl+L; Ctrl+Shift+P (do it near some brackets)
Ctrl+Shift+/;
Ctrl+Shift+Y and Ctrl+Shift+X (do it on a word or variable name
e.g.)
Alt+Down; Alt+Up
3. To make sure you didnt do any damage,
Select any source files you changed and do rightmouse > replace with ..
(if you made project from CVS) .Latest from HEAD
(If you made project from remote files) Local History .
Observe that your changes are gone.
Editor Features
Editor-16
MPI Programming
Objective
Learn about MPI features for your source files
Contents
Using Editor features for MPI
MPI Help features
Finding MPI Artifacts
MPI New Project Wizards
MPI Barrier Analysis
MPI Programming
MPI-0
MPI-Specific Features
PTPs Parallel Language Development Tools (PLDT) has
several features specifically for developing MPI code
Show MPI Artifacts
Code completion / Content Assist
Context Sensitive Help for MPI
Hover Help
MPI Templates in the editor
PLDT has similar features for OpenMP, UPC,

OpenSHMEM, OpenACC
MPI Programming
MPI-1
Show MPI Artifacts

In Project Explorer, select a project, folder, or a
single source file
The analysis will be run on the selected resources
Run the analysis by

clicking on dropdown menu next to
the analysis button
Select Show MPI
Artifacts
Works on local and

remote files
MPI Programming
MPI-2
-2
MPI Artifact View

Markers indicate the
location of artifacts in
editor
The MPI Artifact View
lists the type and location
of each artifact
Navigate to source code
line by double-clicking on
the artifact
Run the analysis on
another file (or entire
project!) and its markers
will be added to the view
Click on column headings
to sort
Remove markers via
MPI Programming
MPI-3
-3
MPI Editor Features

Code completion will show all
the possible MPI keyword
completions
Enter the start of a keyword
then press <ctrl-space>
Hover over MPI API

Displays the function
prototype and a
description
MPI Programming
MPI-4
-4
Context Sensitive Help

Click mouse, then press help
key when the cursor is within a
function name
Windows: F1 key
Linux: ctrl-F1 key
MacOS X: Help key or
HelpDynamic Help
A help view appears (Related

Topics) which shows
additional information
(You may need to click on MPI
API in editor again, to
populate)
Click on the function name to
see more information
Move the help view within your
Eclipse workbench, if you like,
by dragging its title tab
MPI Programming
Some special
info has been
added for MPI
APIs
MPI-5
-5
MPI Templates
Allows quick entry of common patterns in MPI programming
Example:
MPI send-receive
Enter:
mpisr <ctrl-space>
Expands to a send-receive
pattern
Highlighted variable names
can all be changed at once
Type mpi <ctrl-space> <ctrlspace> to see all templates
Add more templates using Eclipse preferences!

C/C++>Editor>Templates
Extend to other common patterns
MPI Programming
MPI-6
-6

Verify barrier
synchronization in C/MPI
programs
For verified programs, lists
barrier statements that
synchronize together
(match)
For synchronization
errors, reports counter
example that illustrates
and explains the error
Local files only
MPI Programming
MPI-7
MPI Barrier Analysis (2)

Run the Analysis:
In the Project
Explorer, select the
project (or directory,
or file) to analyze
Select the MPI
Barrier Analysis
action in the pulldown menu
MPI Programming
MPI-8
MPI Barrier Analysis (3)

No Barrier Errors are found (no pop-up
indicating error)
Two barriers are found
MPI Programming
MPI-9
MPI Barrier Analysis Views
MPI Barriers view
Barrier Matches view

Simply lists the barriers Groups barriers that
match together in a
Like MPI Artifacts view, barrier set all
double-click to navigate processes must go
to source code line (all through a barrier in the
3 views)
set to prevent a
deadlock
Barrier Errors view

If there are errors, a
counter-example
shows paths with
mismatched number
of barriers
MPI Programming
MPI-10
Barrier Errors
Lets cause a barrier mismatch error
Open worker.c in the editor by double-clicking
on it in Project Explorer
At about line 125,
enter a barrier:
Type MPI_B
Hit Ctl-space
Select MPI_Barrier
Add communicator
arg MPI_COMM_WORLD
MPI Programming
and closing semicolon
MPI-11
Barrier Errors (2)

Save the file
Ctl-S (Mac Command-S) or File > Save
Tab should lose asterisk indicating file saved
Run barrier analysis on shallow project again

Select shallow
project in Project
Explorer first
MPI Programming
MPI-12
Barrier Errors (3)

Barrier Error is found
Hit OK to dismiss dialog
Code diverges on line 87
One path has 2 barriers, other has 1
Double-click
on a row in
Barrier Errors
view to find
the line it
references in
the code
MPI Programming
MPI-13
Fix Barrier Error

Fix the Barrier Error
before continuing
Double-click on the
barrier in worker.c
to quickly navigate
to it
Remove the line and save the file
Re-run the barrier analysis to check that it has
been fixed
MPI Programming
MPI-14
Remove Barrier Markers

Run Barrier Analysis again to remove the error
Remove the Barrier Markers via the X in one
of the MPI Barrier views
MPI Programming
MPI-15
MPI New Project Wizards

Quick way to make a simple MPI project
File > New > C Project
MPI Hello World
is good for trying out
Eclipse for MPI
MPI Features for

Eclipse
MPI-16
MPI New Project Wizards (2)

Next> and fill in (optional) Basic Settings
Next> and fill in MPI Project
Settings
Include path set in MPI
Preferences can be added to
project
MPI Features for

Eclipse
MPI-17
MPI New Project Wizards (3)

Select Finish and MPI Hello World project
is created
MPI Features for

Eclipse
MPI-18
MPI Preferences
Settings for MPI New Project wizards
MPI Include paths, if set in MPI
Preferences, are added in MPI New
Project Wizard
MPI Features for

Eclipse
MPI-19
10
Exercise
1. Find MPI artifacts in shallow project
Locate all the MPI communication (send/receive)
calls
2. Use content assist to add an api call

E.g., Type MPI_S, hit ctl-space
3. Use hover help

4. Use a template to add an MPI code template
On a new line, type mpisr and ctl-space
MPI Programming
MPI-20
Optional Exercise
1. Insert an MPI_Barrier function call into one of
your source files using content assist
E.g. Line 125 of worker.c
2. Save the file

3. Run Barrier Analysis on the project
4. Locate the source of the barrier error and
remove the statement
5. Re-run barrier analysis to observe that the
problem has been fixed
MPI Programming
MPI-21
11
Building a Project
Objective
Learn how to build an MPI program on a remote
system
Contents
How
How
How
How
to
to
to
to
change build settings

start a build and view build output
clean and rebuild a project
create build targets
Building a Project
Build-0
Synchronizing the Project

Prior to Build
Because we will be running on a remote
system, we must also build on that system
Source files must be available to build
We have already created a synchronized
project to do this
Files are synchronized automatically when
they are saved
A full synchronize is also performed prior to a
build
Build
Build-1
Active Build Configuration

The Active build configuration determines which
system will be used for both synchronizing and building
Since this is a
Synchronized
Project, the
remote target
will be the Active
Build
Configuration by
default
Right mouse on
Project
Next slide confirms where

this is.
Build-2
Build
Confirm Active Build

Configuration
Where is my project going to build?
To confirm where each build configuration is located:
In Project Properties*, under C/C++ Build, select
Synchronize. You should see the remote connection
and file location
* To see Project
Properties: in Project
Explorer view, right mouse
on project and select
Properties at the
bottom of the context
menu
Build
Build-3
Start with clean shallow

Start with original shallow code:
Project checked out from CVS:
Right mouse on project,
Replace with > Latest from HEAD
Changed file:
Also see Compare With

Other project:
Restore from local history finds deleted files
Right mouse on file, Compare With
or Replace With
Build-4
Building a Project
Starting the Build

Select the project in Project Explorer
Click on the
hammer button in toolbar to run a build
using the active build configuration
By default, the Build Configuration assumes there is a

Makefile (or makefile) for the project
Building a Project
Build-5
Viewing the Build Output

Build output will be visible in console
Building a Project
Build-6
Build Problems
Build problems will be
shown in a variety of
ways
Marker on file
Marker on editor line
Line is highlighted
Marker on overview ruler
Listed in the Problems
view
Double-click on line in
Problems view to go
to location of error in
the editor
Building a Project
Build-7
Forcing a Rebuild
If no changes have been made,
make doesnt think a build is needed
e.g. if you only change the Makefile
In Project Explorer, right click on
project; Select Clean Project
Build console will display results
Rebuild project by clicking on

build button again
Building a Project
Build-8
Forcing a Resync
Project should resync with remote
system when things change
Sometimes you may need to
do it explicitly
Synchronization>Sync Active Now
Status area in lower right shows
when Synchronization occurs
Building a Project
Build-9
Creating Make Targets

By default
The build button will run make all
Cleaning a project will run make clean
Sometimes, other build targets are

required
Open Make Target view
Select project and click on New
Make Target button
Enter new target name
Modify build command if desired
New target will appear in view
Double click on target to activate
Building a Project
Build-10
Build Configuration
The build configuration is specified in the project properties
Open the properties by right-clicking on the project name in the Project
Explorer view and selecting Properties (bottom of the context menu
list)
C/C++ Build
Configure the build command
Default is make but this can be
changed to anything
C/C++ Build > Settings

Binary and Error parser selection
Tool Chain settings (managed projects
only)
C/C++ Build > Environment

Modify/add environment variables passed
to build
C/C++ Build > Logging

Enable/disable build logging
Building a Project
Build-11
Selecting Build Configuration

Multiple build configurations may be available
Remote and local build configuration
Build configurations for different architectures
The active build configuration is set from the Build

Configurations project context menu
Right click on project, then select the build configuration from the
Build Configurations > Set Active menu
Building a Project
Build-12
Configuring Build Modules

If the remote system
has Modules installed, a
custom set of modules
can be configured for
building C/C++
projects
In the project
properties, navigate to
C/C++ Build >
Environment
Management
Check Use an
environment
management system
to customize the
remote build
environment
Building a Project
Build-13
Configuring Build Modules (2)

Select modules
from the list
Use the Filter

list field to
quickly find
modules with a
given name
Click Select Defaults to check only those modules that are

present in a new Bash login shell
Building a Project
Build-14
Configuring Build Modules (3)

To build the project, Eclipse will
Open a new Bash login shell

Execute module purge
Execute module load for each selected module
Run make
Module commands are displayed in the Console view during build

Beware of modules that must be loaded in a particular order, or
that contain common paths like /bin or /usr/bin
Building a Project
Build-15
Configuring Build Modules: SEA

Right click on
Project, select
project properties
C/C++ Build,
Environment
Management
Select Use an
environment
management system..
Select Manually
specify
environment
Add string and then hit OK
module purge >/dev/null 2>&1;module load intel/12.1.5;module load
ncarbinlibs/1.0;module load ncarcompilers/1.0;module load ncarenv/1.0;module load
Build-16
Building a Project
netcdf/4.2;module
load workshop;module load tau
Exercise
1. Start with your shallow project
2. Build the project
3. Edit a source file and introduce a compile error
In main.c, line 97, change ; to :
Save, rebuild, and watch the Console view
Use the Problems view to locate the error
Locate the error in the source code by double
clicking on the error in the Problems view
Fix the error
4. Rebuild the project and verify there are no build errors
Building a Project
Build-18
Optional Exercise
1. Open the Makefile in Eclipse. Note the line starting with
tags: this defines a make target named tags.
2. Open the Outline view while the Makefile is open. What icon
is used to denote make targets in the Outline?
3. Right-click the tags entry in the Outline view. Add a Make
Target for tags.
4. Open the Make Targets view, and build the tags target.
5. Rename Makefile to Makefile.mk

6. Attempt to build the project; it will fail
7. In the project properties (under the C/C++ Build category),
change the build command to: make f Makefile.mk
8. Build the project; it should succeed
Building a Project
Build-19
10
Running an Application
Objective
Learn how to run an MPI program on a remote system
Contents
Creating a run configuration
Configuring the application run
Monitoring the system and jobs
Controlling jobs
Obtaining job output
Run-0
Creating a Run Configuration
Open the run configuration

dialog Run>Run
Configurations
Select Parallel Application
Select the New button
Or, just double-click on
Parallel Application
to create a new one
Note: We use Launch Configuration as a generic term to refer to either a

Run Configuration or a Debug Configuration, which is used for debugging.
Run-1
Set Run Configuration Name

Enter a name for this run configuration
E.g. shallow
This allows you to easily re-run the same application
Run-2
-2
Configuring the Target System

In Resources tab, select
a Target System
Configuration that
corresponds to your target
system
The tutorial instructor will
indicate what Target System
Configuration to select
SEA: use
IBM Platform LSF
Target system
configurations can be
generic or can be specific
to a particular system
Use the specific
configuration if available,
or the generic
configuration that most
closely matches your
system
Run-3
-3
Configure the Connection

Choose a connection to
use to communicate with
the target system
If no connection has been
configured, click on the
New button to create a
new one
Fill in connection information,
then click ok
The new connection

should appear in the
dropdown list
SEA: Select the
connection you already
have to
yellowstone.ucar.edu
Run-4
-4
Resources Tab
The content of the
Resources tab will vary
depending on the target
system configuration
selected
This example shows the
IBM Platform LSF
configuration
For the SEA workshop,
we will indicate the
settings that need to be
set on the next slide
Run-5
-5
LSF Settings for SEA Tutorial

Description
Value
Exclusive Execution
false
Job is Resizable
false
Dont Rerun on system failure
True
Completion_Notification
false
Dispatch_Notification
false
Number of Processors
Pass User Limits
True
Project Name
SCSG004
Job Queue
tutorial
Pull down menu
Rerun on System Failure
false
Estimated Runtime
30
Runtime Limit:
30
STDERR Path (Append)
/glade/u/home/jalameda/shallow03apr2013-test/
Your project directory

STDOUT Path (Append)
/glade/u/home/jalameda/shallow03apr2013-test/
Running
an Application
MPI Command
mpirun.lsf
Run-6
Viewing the Job Script

Some target
configurations will
provide a View Script
button
Click on this to view the
job script that will be
submitted to the job
scheduler
Batch scheduler
configurations should
also provide a means of
importing a batch script
Run-7
-7
Application Tab
Select the Application
tab
Choose the
Application program
by clicking the Browse
button and locating the
executable on the
remote machine
Use the same
shallow executable
Select Display output

from all processes in
a console view
Run-8
-8
Arguments Tab (Optional)

The Arguments tab lets
you supply command-line
arguments to the
application
You can also change the
default working directory
when the application
executes
Run-9
-9
Environment Tab (Optional)

The Environment tab
lets you set environment
variables that are passed
to the job submission
command
This is independent of the
Environment Management
(module/softenv) support
described in a separate
module
Run-10
-10
Synchronize Tab (Optional)

The Synchronize tab lets
you specify
upload/download rules
that are execute prior to,
and after the job
execution
Click on the New
upload/download rule
buttons to define rules
The rule defines which file
will be
uploaded/downloaded and
where it will be put
Can be used in
conjunction with program
arguments to supply input
data to the application
Run-11
-11
Common Tab (Optional)

The Common tab is
available for most launch
configuration types (not
just Parallel Application)
Allows the launch
configuration to be
exported to an external
file
Can add the launch
configuration to the
favorites menu, which is
available on the main
Eclipse toolbar
Select Run to launch
the job
Run-12
-12
Run
Select Run to launch the job
You may be asked to switch to the System
Monitoring Perspective
Select Remember my decision so you

wont be asked again
Select Yes to switch and launch the job
Building and Running
Run-13
System Monitoring Perspective

System view
Jobs running
on system
Active jobs
Inactive jobs
Messages
Console
Scroll to see more
Run-14
Moving views
The System Monitoring Perspective overlaps
the Active Jobs and Inactive Jobs views
To split them apart and see both at once,
drag the tab for the Inactive Jobs view to
the lower half of its area, and let go of mouse
Building and Running
Run-15
System Monitoring
System view, with
abstraction of system
configuration
Hold mouse button
down on a job in
Active Jobs view to
see where it is
running in System
view
Hover over node in
System view to see
job running on node
in Active Jobs view
Pull down to filter
jobs, or select your
own
One node with

16 cores
Run-16
-16
Job Monitoring
Job initially appears in
Inactive Jobs view
Moves to the Active Jobs
view when execution
begings
Returns to Inactive Jobs
view on completion
Status refreshes
automatically every 60 sec
Can force refresh with menu
Run-17
-17
Controlling Jobs
Right click on a job to open
context menu
Actions will be enabled IFF
The job belongs to you
The action is available on the
target system
The job is in the correct state for
the action
When job has COMPLETED, it

will remain in the Inactive
Jobs view
Run-18
-18
Obtaining Job Output

After status changes to
COMPLETED, the output is
available
Right-click on the job
Select Get Job Output to display
output sent to standard output
Select Get Job Error to retrieve
output sent to standard error
SEA: output/error will be in
project directory, force
synchronization to see
Output/Error info shows in

Console View
Jobs can be removed by
selecting Remove Job Entry
Run-19
-19
10
Add a Monitor
You can monitor other systems too
In Monitors view, select the + button to
add a monitor
Choose monitor type and connection;

create a new connection if necessary
Double click
new monitor
to start
Run-20
Exercise
1.
2.
3.
4.
5.
6.
Start with your shallow project

Create a run configuration
Complete the Resources tab
Select the executable in the Application tab
Submit the job
Check the job is visible in the Inactive Jobs view,
moves to the Active Jobs view when it starts running
(although it may be too quick to show up there), then
moves back to the Inactive Jobs view when completed
7. View the job output
8. Remove the job from the Inactive Jobs view
Run-21
11
Fortran
Objectives
Learn how to create and convert Fortran projects
Learn to use Fortran-specific editing features
Learn about Fortran-specific properties/preferences
Contents
Fortran projects
Using the Fortran editor
Fortran project properties and workbench preferences
Prerequisites
Basics (for exercises)
Fortran Projects
Fortran-0
Ralph Johnsons research group at UIUC used to meet at Pho-Tran
which became the name of their Fortran IDE.
Configuring Fortran Projects
Fortran Projects
Fortran-3
Project Properties
Right-click Project
Select Properties
Project properties are settings

that can be changed for each
project
Contrast with
workspace preferences,
which are the same
regardless of what
project is being edited
e.g., editor colors
Set in Window
Preferences
(on Mac, Eclipse
Preferences)
Careful! Dialog is
very similar
Fortran Projects
Fortran-4
Converting to a Fortran Project

Are there categories labeled Fortran General
and Fortran Build in the project properties?
No Fortran categories
Do this
once
If not, the project is not a Fortran Project

Switch to the Fortran Perspective
In the Fortran Projects view, right-click on the
project, and click Convert to Fortran Project
Dont worry; its still a C/C++ project, too
Every Fortran project is also a C/C++ Project

Fortran Projects
Fortran-5
Project Location
How to tell where a project
resides?
In the project properties
dialog, select the
Resource category
Fortran Projects
Fortran-6
Error Parsers
Are compiler errors not appearing in the
Problems view?
Make sure the correct error parser is enabled
In the project properties, navigate to
C++ BuildSettings or Fortran BuildSettings
Switch to the Error Parsers tab
Check the error parser(s) for your compiler(s)
Fortran Projects
Do this
once
Fortran-7
Fortran Source Form Settings

Fortran files are either free form or fixed form;
some Fortran files are preprocessed (#define, #ifdef, etc.)
Source form determined by filename extension
Defaults are similar to most Fortran compilers:
Fixed form:
.f
.fix
.for
.fpp
Free form:
.f08
.F08
.f03
.F03
.f95
.F95
.f90
.F90
.ftn
.f77
< unpreprocessed
< preprocessed
Many features will not work if filename extensions

are associated with the wrong source form
(outline view, content assist, search, refactorings, etc.)
Fortran Projects
Fortran-8
Fortran Source Form Settings

Do this
once
In the project
properties, select
Fortran General
Source Form
Select source form
for each filename
extension
Click OK
Fortran Projects
Fortran-9
Enabling Fortran Advanced Features

Some Fortran features are disabled by default
Must be explicitly enabled
Do this
once
In the project properties dialog,

select Fortran General Analysis/Refactoring
Click Enable
Analysis/
Refactoring
Close and re-open
any Fortran editors
This turns on the

Photran Indexer
Turn it off if its slow
Fortran Projects
Fortran-10
Exercise
1. Convert shallow to a Fortran project
2. Make sure errors from the GNU Fortran
compiler will be recognized
3. Make sure *.f90 files are treated as
Free Form which is unpreprocessed
4. Make sure search and refactoring will work in
Fortran
Fortran Projects
Fortran-11
Advanced Editing
Code Templates
Fortran Projects
Fortran-12
Code Templates
(C/C++ and Fortran)
Auto-complete common code patterns

For loops/do loops, if constructs, etc.
Also MPI code templates
Included with content assist proposals
(when Ctrl-Space is pressed)

E.g., after the last line in tstep.f90, type sub and
press Ctrl-Space
Press Enter to insert the template
Fortran Projects
Fortran-13
Code Templates (2)

(C/C++ and Fortran)
After pressing enter to insert the code

template, completion fields are highlighted
Press Tab to move between completion fields

Changing one instance of a field changes all
occurrences
Fortran Projects
Fortran-14
Exercise
Open tstep.f90 and retype the last loop nest
Use the code template to complete the do-loops
Use content assist to complete variable names
Fortran Projects
Fortran-15
Custom Code Templates

(Fortran)
Customize code templates in Window

Preferences Fortran Templates
Can import/export templates to XML files

Fortran Projects
Fortran-16
Search & Refactoring

Objectives
Develop proficiency using Eclipses textual and
language-based search and navigation capabilities
Introduce common automated refactorings
Contents
Searching
Refactoring and Transformation
Prerequisites
Basics
Fortran
Advanced Features
Advanced-0
Find/Replace within Editor

Simple Find within editor buffer
Ctrl-F (Mac: Command-F)
Advanced Features
Advanced-1
Mark Occurrences
(C/C++ Only)
Double-click on a variable in the CDT editor

All occurrences in the source file are
highlighted to make locating the variable
easier
Alt-shift-O to turn off (Mac: Alt-Cmd-O)
Advanced Features
Advanced-2
Language-Based Searching
(C/C++ and Fortran)
Knows what things can

be declared in each
language (functions,
variables, classes,
modules, etc.)
Advanced Features
E.g., search for every call

to a function whose name
starts with get
Search can be project- or
workspace-wide
Advanced-3
Find References
(C/C++ and Fortran)
Finds all of the places where a variable,

function, etc., is used
Right-click on an identifier in the editor
Click ReferencesWorkspace
or ReferencesProject
Search view
shows matches
Advanced Features
Advanced-4
Open Declaration
(C/C++ and Fortran)
Jumps to the declaration of

a variable, function, etc.,
even if its in a different
file
Left-click to select identifier
Right-click on identifier
Click Open Declaration
C/C++ only:
Can also Ctrl-click
(Mac: Cmd-click) on an
identifier to hyperlink to
its declaration
Advanced Features
Goes to its declaration

in copy.c
Advanced-5
Search Try It!

1. Find every call to MPI_Recv in Shallow.
2. In worker.c, on line 42, there is a declaration
float p[n][m].
a) What is m (local? global? function parameter?)
b) Where is m defined?
c) How many times is m used in the project?
3. Find every C function in Shallow whose name

contains the word time
Advanced Features
Advanced-6
Refactoring and Transformation
Advanced Features
Advanced-7
Refactoring
(making changes to source code that dont affect the behavior of the program)
Refactoring is the research

motivation for Photran @ Illinois
Illinois is a leader in refactoring research
Refactoring was coined in our group
(Opdyke & Johnson, 1990)
We had the first dissertation

(Opdyke, 1992)
and built the first refactoring tool

(Roberts, Brant, & Johnson, 1997)
and first supported the C preprocessor

(Garrido, 2005)
Photrans agenda: refactorings for HPC,

language evolution, refactoring framework
Photran 7.0: 31 refactorings
Advanced Features
Advanced-8
Refactoring Caveats
Photran can only refactor free form code that
is not preprocessed
Determined by Source Form settings
(recall from earlier that these are configured in
Project Properties: Fortran GeneralSource Form)
Free Form, Unpreprocessed: .f08
.f03
.f95
.f90
Free Form, Preprocessed:
.F08
.F03
.F95
.F90
Fixed Form:
.for
.fpp
.ftn
.f77
.f
.fix
Refactor menu will be empty if

Refactoring not enabled in project properties
(recall from earlier that it is enabled in
Project Properties: Fortran GeneralAnalysis/Refactoring)
The file in the active editor is fixed form

The file in the active editor is preprocessed
Advanced Features
Advanced-9
Rename Refactoring
(also available in Fortran)
Changes the name of a variable, function,

etc., including every use
(change is semantic, not textual, and can be workspace-wide)
Only proceeds if the new name will be legal

(aware of scoping rules, namespaces, etc.)
In Java (Murphy-Hill et al., ICSE 2008):
Switch to C/C++ Perspective

Open a source file
In the editor, click on a
variable or function name
Select menu item
RefactorRename
Or use context menu
Enter new name
Advanced Features
Advanced-10
Rename in File
(C/C++ Only)
Position the caret

over an identifier.
Press Ctrl-1
(Command-1 on Mac).
Enter a new name.

Changes are
propagated within
the file as you type.
Advanced Features
Advanced-11
Extract Function Refactoring

(also available in Fortran - Extract Procedure)
Moves statements into a new function, replacing the

statements with a call to that function
Local variables are passed as arguments
Select a sequence of
statements
Select menu item
Refactor
Extract Function
Enter new name
Advanced Features
Advanced-12
Introduce IMPLICIT NONE Refactoring

Fortran does not require variable declarations
(by default, names starting with I-N are integer variables; others are reals)
This adds an IMPLICIT NONE statement and adds explicit

variable declarations for all implicitly declared variables
Introduce in a single file by
opening the file and selecting
RefactorCoding Style
Introduce IMPLICIT NONE
Introduce in multiple files by
selecting them in the Fortran
Projects view, right-clicking on
the selection, and choosing
RefactorCoding
StyleIntroduce IMPLICIT
NONE
Advanced Features
Advanced-13
Loop Transformations
(Fortran only)
Interchange Loops
CAUTION: No check for behavior preservation
Swaps the loop headers in a two-loop nest

Select the loop nest, click menu item RefactorDo Loop
Interchange Loops (Unchecked)
Old version traverses

matrices in row-major order
Advanced Features
New version traverses

in column-major order
(better cache performance)Advanced-14
Loop Transformations
(Fortran only)
Unroll Loop
Select a loop, click RefactorDo LoopUnroll Loop
do i = 1, 10
print *, 10*i
end do
Unroll 4
do i = 1, 10, 4
print *, 10*i
print *, 10*(i+1)
print *, 10*(i+2)
print *, 10*(i+3)
end do
Advanced Features
Advanced-15
Refactoring & Transformation

Exercises
In tstep.f90
1. In init.c, extract the printf statements at
the bottom of the file into a new function
called print_banner
2. In worker.c, change the spellings of
neighbour_send and neighbour_receive
to American English
3. In tstep.f90, make the (Fortran) tstep
subroutine IMPLICIT NONE
Advanced Features
Advanced-16
NCSA/XSEDE Features
Objectives
Install NCSAs GSI auth and XSEDE support plug-ins
Become familiar with the System menu
Contents
Capabilities
Installation
Prerequisites
(none)
Advanced Features: NCSA/XSEDE
NCSA-0
Additional Plug-ins from NCSA

NCSA publishes additional plug-ins can be
added onto an existing PTP installation
Contribute a System menu to the menu bar
with XSEDE- and NCSA-specific commands
NCSA-1
System Menu
Open Web content in Eclipse:
Open XSEDE User Portal
Open User Guide for a machine
Open an SSH terminal

(as an Eclipse view)
Eclipse-integrated SSH terminals are provided

by the Remote System Explorer (RSE), one of
the features that is included in the Eclipse for
Parallel Application Developers package.
NCSA-2
System Menu
Shortcuts for common PTP tasks:
Add Remote Environment adds a
Remote Tools connection for a
particular machine
Add System Monitor opens the
System Monitoring perspective and
begins monitoring a particular
machine
NCSA-3
System Menu
The plug-in is preconfigured with
information about XSEDE and
NCSA resources
The bottom four commands
generally prompt for a system
Select System can be used to
eliminate this prompt, so these
commands always act on a
particular system
NCSA-4
MyProxy Logon
MyProxy Logon allows you
to authenticate with a
MyProxy server
Often myproxy.teragrid.org
It stores a credential, which

is usually valid for 12 hours
During these 12 hours, SSH
connections to XSEDE
resources will not require a
password; they can use the
stored credential
However, you must enter the
correct username for that
machine!
NCSA-5
Installation
1. Click Help > Install New Software
2. Click Add to open the Add Repository dialog
3. In the Location field, enter
http://forecaster.ncsa.uiuc.edu/updates/juno
and then click OK to close the Add dialog.
Or, if you copied ncsa-update-size.zip from a USB

drive, click Archive, select that file, and click OK.
4. Select the following:

GSI Authentication and MyProxy Logon Support
NCSA and XSEDE System Support
5. Click Next and complete the installation

NCSA-6
Configuring SSH Tunnel
SSH Tunnel
Tunnel-0
Configure the
Synchronized Project SSH tunnel (1)
If your machine access requires ssh access through a
frontend/intermediate node, set up an ssh tunnel before configuring
the project - from command line or e.g. Windows PuTTY, e.g.
ssh -L <port>:<target-host> <userid>@<frontend-host>
(For details see http://wiki.eclipse.org/PTP/FAQ)
When you configure the connection for the project

Connection: New
The connection will use
the port for the ssh tunnel
(details on next slide)
SSH Tunnel
Tunnel-1
Configure connection to
remote host SSH Tunnel (2)
In Target Environment Configuration
dialog, enter target name,
and host information
1. Specify Target name
2. If using a tunnel, select
Localhost and enter userid and
password for remote system
For direct access, just
select Remote Host, enter
hostname, userid,
password
3. select the Advanced button
to specify the port
Select Finish
1.
2.
3.
Specify port for tunnel
SSH Tunnel
Tunnel-2
Parallel Debugging
Objective
Learn the basics of debugging parallel programs
Contents
Launching a debug session
The Parallel Debug Perspective
Controlling sets of processes
Controlling individual processes
Parallel Breakpoints
Terminating processes
Parallel Debugging
Debug-0
Debugging Setup
Debugging requires interactive access to the application
Can use any of the -Interactive target configurations
Torque-Generic-Interactive
PBS-Generic-Interactive
OpenMPI-Generic-Interactive
Parallel Debugging
Debug-1
Create a Debug Configuration
A debug configuration is
essentially the same as a run
configuration (like we used
in the Running an
Application module)
It is possible to re-use an
existing configuration and
add debug information
Use the drop-down next to
the debug button (bug icon)
instead of run button
Select Debug
Configurations to open
the Debug Configurations
dialog
Parallel Debugging
Debug-2
Create a New Configuration

Select the existing
configuration
Click on the new button to
create a new configuration
Parallel Debugging
Debug-3
Configure the Resources Tab

Select the new
target system
configuration
Choose the queue
Make sure number of
nodes is correct
Make sure the
mpirun command is
selected
Select the number of
processes (in this
case use 5)
Parallel Debugging
Debug-4
Configure the Debug Tab

Select Debugger
tab
Choose gdb-mi for
the Debugger
backend
Click Browse and
select sdm in your
home directory
Click Ok
Make sure the
debugger path is
correct
Click on Debug to
launch the program
Parallel Debugging
Debug-5
Exercise
1. Open the debug configuration dialog
2. Create a new configuration
3. Select the edu.sdsc.trestles.torque.interactive.openmpi
target configuration
4. Configure the Debug tab
Queue: shared
Number of nodes: 1:ppn=5
MPI Command: mpirun
MPI Number of Processes: 5
5. Launch the debugger
Parallel Debugging
Debug-6
The Parallel Debug Perspective (1)

Parallel Debug
view shows job
and processes
being debugged
Debug view shows
threads and call
stack for individual
processes
Source view
shows a current
line marker for all
processes
Parallel Debugging
Debug-7
The Parallel Debug Perspective (2)

Breakpoints view
shows breakpoints
that have been set
(more on this later)
Variables view
shows the current
values of variables
for the currently
selected process in
the Debug view
Outline view (from
CDT) of source
code
Parallel Debugging
Debug-8
Stepping All Processes

The buttons in the
Parallel Debug View
control groups of
processes
Click on the Step Over
button
Observe that all process
icons change to green,
then back to yellow
Notice that the current
line marker has moved to
the next source line
Parallel Debugging
Debug-9
Stepping An Individual Process

The buttons in the
Debug view are used
to control an
individual process, in
this case process 0
Click the Step Over
button
You will now see two
current line markers,
the first shows the
position of process 0,
the second shows the
positions of processes
1-3
Parallel Debugging
Debug-10
Process Sets (1)

Traditional debuggers apply operations to a single
process
Parallel debugging operations apply to a single process
or to arbitrary collections of processes
A process set is a means of simultaneously referring to
one or more processes
Parallel Debugging
Debug-11
Process Sets (2)

When a parallel debug session is first started, all
processes are placed in a set, called the Root set
Sets are always associated with a single job
A job can have any number of process sets
A set can contain from 1 to the number of processes in
a job
Parallel Debugging
Debug-12
Operations On Process Sets

Debug operations on the
Parallel Debug view
toolbar always apply to the
current set:
Resume, suspend, stop,
step into, step over, step
return
The current process set is

listed next to job name
along with number of
processes in the set
The processes in process
set are visible in right hand
part of the view
Parallel Debugging
Root set = all processes
Debug-13
Managing Process Sets

The remaining icons in the toolbar of the Parallel
Debug view allow you to create, modify, and delete
process sets, and to change the current process set
Create set
Remove
from set
Change
current set
Delete
set
Parallel Debugging
Debug-14
Creating A New Process Set

Select the processes
you want in the set by
clicking and dragging,
in this case, the last
three
Click on the Create
Set button
Enter a name for the
set, in this case
workers, and click OK
You will see the view
change to display only
the selected processes
Parallel Debugging
Debug-15
Stepping Using New Process Set

With the workers set
active, click the Step
Over button
You will see only the
first current line
marker move
Step a couple more
times
You should see two line
markers, one for the
single master process,
and one for the 3
worker processes
Parallel Debugging
Debug-16
Process Registration
Process set commands apply to groups of
processes
For finer control and more detailed
information, a process can be registered and
isolated in the Debug view
Registered processes, including their stack
traces and threads, appear in the Debug
view
Any number of processes can be registered,
and processes can be registered or
un-registered at any time
Parallel Debugging
Debug-17
Process Registration (2)

By default, process 0 was
registered when the debug
session was launched
Registered processes are
surrounded by a box and
shown in the Debug view
The Debug view only shows

registered processes in the
current set
Since the workers set
doesnt include process 0, it
is no longer displayed in the
Debug view
Parallel Debugging
Debug-18
Registering A Process
To register a process,
double-click its process
icon in the Parallel
Debug view or select a
number of processes and
click on the register
button
Groups (sets)
of processes
Individual
(registered)
processes
To un-register a process,
double-click on the
process icon or select a
number of processes and
click on the unregister
button
Parallel Debugging
5-19
10
Current Line Marker

The current line marker is used to show the
current location of suspended processes
In traditional programs, there is a single
current line marker (the exception to this is
multi-threaded programs)
In parallel programs, there is a current line
marker for every process
The PTP debugger shows one current line
marker for every group of processes at the
same location
Parallel Debugging
Debug-20
Colors And Markers

The highlight color depends on
the processes suspended at
that line:
Blue: All registered process(es)
Orange: All unregistered
process(es)
Green: Registered or unregistered

process with no source line (e.g.
suspended in a library routine)
The marker depends on the

type of process stopped at that
location
Hover over marker for more
details about the processes
suspend at that location
Parallel Debugging
Multiple processes marker

Registered process marker
Un-registered process marker
Debug-21
11
Exercise
1. From the initial debugger session, step all processes
until the current line is just after MPI_Init (line 68)
2. Create a process set called workers containing
processes 1-4
3. Step the worker processes twice, observe two line
markers
4. Hover over markers to see properties
5. Switch to the root set
6. Step only process 0 twice so that all processes are now
at line 71 (hint use the debug view)
Debug-22
Parallel Debugging
Breakpoints
Apply only to processes in the particular set that is
active in the Parallel Debug view when the breakpoint
is created
Breakpoints are colored depending on the active
process set and the set the breakpoint applies to:
Green indicates the breakpoint set is the same
as the active set.
Blue indicates some processes in the breakpoint set are
also in the active set (i.e. the process sets overlap)
Yellow indicates the breakpoint set is different from the
active set (i.e. the process sets are disjoint)
When the job completes, the breakpoints are

automatically removed
Parallel Debugging
Debug-23
12
Creating A Breakpoint
Select the process set that
the breakpoint should apply
to, in this case, the workers
set
Double-click on the left edge
of an editor window, at the
line on which you want to set
the breakpoint, or right click
and use the Parallel
BreakpointToggle
Breakpoint context menu
The breakpoint is displayed
on the marker bar
Parallel Debugging
Debug-24
Hitting the Breakpoint

Switch back to the Root set
by clicking on the Change
Set button
Click on the Resume button
in the Parallel Debug view
In this example, the three
worker processes have hit the
breakpoint, as indicated by
the yellow process icons and
the current line marker
Process 0 is still running as its
icon is green
Processes 1-3 are suspended
on the breakpoint
Parallel Debugging
Debug-25
13
More On Stepping
The Step buttons are only
enabled when all processes
in the active set are
suspended (yellow icon)
In this case, process 0 is still
running
Switch to the set of

suspended processes (the
workers set)
You will now see the Step
buttons become enabled
Parallel Debugging
Debug-26
Breakpoint Information
Hover over breakpoint icon
Will show the sets this breakpoint applies to
Select Breakpoints view

Will show all breakpoints in all projects
Parallel Debugging
Debug-27
14
Breakpoints View
Use the menu in the breakpoints view to
group breakpoints by type
Breakpoints sorted by breakpoint set (process
set)
Parallel Debugging
Debug-28
Global Breakpoints
Apply to all processes and all jobs
Used for gaining control at debugger startup
To create a global breakpoint
First make sure that no jobs are selected (click in white
part of jobs view if necessary)
Double-click on the left edge of an editor window
Note that if a job is selected, the breakpoint will apply to
the current set
Parallel Debugging
Debug-29
15
Exercise
1. Select the worker process set
2. Create a breakpoint by double-clicking on right hand
bar at line 88 (worker function)
3. Hover over breakpoint to see properties
4. Switch to root process set
5. Observer breakpoint color changes to blue
6. Resume all processes
7. Observe worker processes at breakpoint, and process
0 still running (green icon)
8. Switch to worker process set
9. Step worker processes over worker() function
10. Observe output from program
Parallel Debugging
Debug-30
Terminating A Debug Session

Click on the Terminate
icon in the Parallel
Debug view to
terminate all processes
in the active set
Make sure the Root set
is active if you want to
terminate all processes
You can also use the

terminate icon in the
Debug view to
terminate the currently
selected process
Parallel Debugging
Debug-31
16
Cancelling The Job

Interactive jobs will continue
until the reservation time has
expired
You can cancel the job once
the debug session is finished
Locate the job in the Active
Jobs view
Use the view menu to filter for
only your jobs if there are too
many
Right click on the job and

select Cancel Job
Parallel Debugging
Debug-32
Exercise
1.
2.
3.
4.
Switch to the root set

Terminate all processes
Switch to the System Monitoring perspective
Right-click on your running job and select Cancel
Parallel Debugging
Debug-33
17
Optional Exercise
1.
2.
3.
4.
5.
6.
7.
8.
Launch another debug job

Create a breakpoint at line 71 in main.c
Resume all processes
Select the Variables view tab if not already selected
Observe value of the tid variable
Register one of the worker processes
Select stack frame of worker process in Debug view
Observe value of the tid variable matches worker
process
9. Switch to the breakpoints view, change grouping
10. Terminate all processes
11. Switch to the System Monitoring perspective and
cancel the job
Parallel Debugging
Debug-34
18
Performance Tuning
and Analysis Tools
Objective
Become familiar with tools integrated with PTP, to help
enhance performance of parallel applications
Contents
Overview of ETFw and Performance Tools
Performance and Analysis

Tools
Perf-0
PTP/External Tools Framework

formerly Performance Tools Framework
Goal:
Reduce the eclipse plumbing
necessary to integrate tools
Provide integration for
instrumentation, measurement, and
analysis for a variety of performance
tools
Dynamic Tool Definitions:

Workflows & UI
Tools and tool workflows are specified in an XML file
Tools are selected and configured in the launch
configuration window
Output is generated, managed and analyzed as
specified in the workflow
One-click launch functionality
Support for development tools such as TAU, PPW and
others.
Adding new tools is much easier than developing a full
Eclipse plug-in
Performance and Analysis Tools
Perf-1
4/3/2013
Performance Tuning
and Analysis Tools - TAU
Objective
Become familiar with tools integrated with PTP, to help
enhance performance of parallel applications
Contents
Performance Tuning and external tools:
PTP External Tools Framework (ETFw), TAU
Hands-on exercise using TAU with PTP
TAU
TAU-1
TAU: Tuning and Analysis Utilities

TAU is a performance evaluation tool
It supports parallel profiling and tracing
Profiling shows you how much (total) time was spent in each routine
Tracing shows you when the events take place in each process along
a timeline
TAU uses a package called PDT (Performance Database Toolkit) for

automatic instrumentation of the source code
Profiling and tracing can measure time as well as hardware
performance counters from your CPU (or GPU!)
TAU can automatically instrument your source code (routines, loops,
I/O, memory, phases, etc.)
TAU runs on all HPC platforms and it is free (BSD style license)
TAU has instrumentation, measurement and analysis tools
paraprof is TAUs 3D profile browser
TAU
TAU-2
4/3/2013
TAU Performance System Architecture
TAU
TAU-3
PTP TAU plug-ins

http://www.cs.uoregon.edu/research/tau
TAU (Tuning and Analysis Utilities)

First implementation of External Tools Framework (ETFw)
Eclipse plug-ins wrap TAU functions, make them available
from Eclipse
Full GUI support for the TAU command line interface
Performance analysis integrated with development
environment
TAU
TAU-4
4/3/2013
TAU Integration with PTP

TAU: Tuning and
Analysis Utilities
Performance data
collection and analysis
for HPC codes
Numerous features
Command line interface
The TAU Workflow:

Instrumentation
Execution
Analysis
TAU
TAU-5
TAU PTP Installation

This tutorial assumes that the TAU extensions for PTP
are installed they are not included in the
Eclipse for Parallel Application Developers
The installation section (Module 1) shows how to install
TAU and other features from the PTP update site
be sure TAU was selected
To confirm:
Help>Install New Software
Select the link What is already
installed at the bottom of the
dialog
You should see the TAU
Extension
TAU
TAU-6
4/3/2013
Installing TAU Analysis Tools

The TAU plugin can use ParaProf for visual analysis and TauDB
for organization of profiles
To install these utilities on Mac or Linux platforms:
Download (browser, curl or wget)
tau.uoregon.edu/tautools.tgz
tar -zxf tautools.tgz
cd tautools-2.22b
./configure
Set path as shown (launch eclipse from this environment)
Run taudb_configure --create-default
Java WebStart: tau.uoregon.edu/paraprof
TAU Installation, downloads and instructions: tau.uoregon.edu
TAU
TAU-7
Assumptions
Obtain and install TAU*
Download at tau.uoregon.edu
The website includes setup and user guides
Set up the $PATH on the remote machine*

For TAU you should be able to run which pprof on a remote login
and see a result from your TAU bin directory
On yellowstone run the following module commands:
module load workshop; module load tau
Include eclipse.inc in the makefile*

Create an empty eclipse.inc file in the same directory as the
makefile
Place include eclipse.inc in the makefile after regular compiler
definitions
ETFw will modify eclipse.inc to set CC/CXX/FC variables
TAU
* SC tutorial: this has been done for you
TAU-8
4/3/2013
Selective Instrumentation
By default tau provides timing data for each
subroutine of your application
Selective instrumentation allows you to
include/exclude code from analysis and control
additional analysis features
Include/exclude source files or routines

Add timers and phases around routines or arbitrary code
Instrument loops
Note that some instrumentation features require the PDT
Right click on calc.c, init.c, diag.c go to the Selective

Instrumention option and select Instrument Loops
Note the creation of tau.selective (refresh if needed)
TAU
TAU-9
Begin Profile Configuration

The ETFw uses the same run configurations and
resource managers as debugging/launching
Click on the Run menu or the right side of the
Profile button
From the dropdown menu select Profile

configurations
TAU
TAU-10
4/3/2013
Select Configuration
Select the shallow configuration
prepared earlier
The Resource and Application
configuration tabs require little or
no modification
Performance Analysis tab is

present in the Profile
Configurations dialog
We are using the same resource

manager and Torque settings
Since we are using a makefile project
the application will be rebuilt in and
run from the previously selected
location
TAU
TAU-11
Select Tool/Workflow
Select the Performance Analysis tab and
choose the TAU tool set in the Select Tool
dropdown box
Other tools may be available, either installed as
plug-ins or loaded from workflow definition XML files
Configuration sub-panes appear depending on the
selected tool
Tabs may be
hidden if the
window is too
small
TAU
TAU-12
4/3/2013
Select TAU Configuration

Choose the TAU Makefile tab:
All TAU configurations in
remote installation are
available
Check MPI and PDT
checkboxes to filter listed
makefiles
Make your selection in the
Select Makefile: dropdown
box
Select Makefile.tau-icpc-papi-mpi-pdt
TAU
TAU-13
Choose PAPI Hardware Counters

When a PAPI-enabled TAU
configuration is selected the PAPI
Counter tool becomes available
Select the Select PAPI Counters
button to open the tool
Open the PRESET subtree
Select PAPI_L1_DCM (Data cache
misses)
Scroll down to select PAPI_FP_INS
(Floating point instructions)
Invalid selections are automatically
excluded
Select OK
TAU
TAU-14
4/3/2013
Compiler Options
TAU Compiler Options
Set arguments to TAU compiler scripts
Control instrumentation and
compilation behavior
Verbose shows activity of compiler
wrapper
KeepFiles retains instrumented source
PreProcess handles C type ifdefs in
fortran
In the Selective Instrumentation tab
select Internal then hit Apply
Scroll to bottom of the Tau Compiler tab
and activate TauSelectFile to use
tau.selective
TAU
TAU-15
Runtime Options
TAU Runtime options
Set environment variables used by
TAU
Control data collection behavior
Verbose provides debugging info
Callpath shows call stack
placement of events
Throttling reduces overhead
Tracing generates execution
timelines
TAU
Hover help
TAU-16
4/3/2013
Working with Profiles

Profiles are uploaded to
selected database
A text summary may be
printed to the console
Profiles may be uploaded to
the TAU Portal for viewing
online
tau.nic.uoregon.edu
Profiles may be copied to
your workspace and loaded
in ParaProf from the
command line. Select Keep
Profiles
TAU
TAU-17
Launch TAU Analysis

Once your TAU launch is
configured select Profile
Notice that the project rebuilds with TAU compiler commands
The project will execute normally but TAU profiles will be generated
TAU profiles will be processed as specified in the launch
configuration.
If you have a local profile database the run will show up in the
Performance Data Management view
Double click the new entry to view in ParaProf
Right click on a function bar and select Show Source Code for
source callback to Eclipse
TAU
TAU-18
4/3/2013
Paraprof
Use ParaProf for profile visualization to identify
performance hotspots
Inefficient sequential computation
Communication overhead
IO/Memory bottlenecks
Load imbalance
Suboptimal cache performance
Compare multiple trials in PerfExplorer to identify

performance regressions and scaling issues
To use ParaProf, install TAU from tau.uoregon.edu or
use Java webstart from tau.uoregon.edu/paraprof
TAU
TAU-19
Exercise
Multi-Trial profile comparison
1. Edit the shallow Makefile, adding -O3 to CFLAGS and FFLAGS
2. Rerun the analysis (Run->Profile Configurations. Hit Profile)
3. A second trial, distinguished by a new timestamp, will be
generated
It will appear in your Performance Data Manager view if a profile
database is available
Also present in the Profile subdirectory of your project directory
If you do not see a Profile directory right click on your project and go
to Synchronization->'Sync All Now'
4. Load the two trials in paraprof (on the command line: paraprof
/path/to/tauprofile.xml)
5. Open Windows->ParaProf Manager
6. Expand your database down to reveal all trials
7. Right click on each trial and click 'Add Mean to Comparison
Window' to visualize the two trials side by side
TAU
TAU-20
10
GEM
Graphical Explorer of MPI Programs
GEM
GEM-0
GEM
Graphical Explorer of MPI Programs
Dynamic verification for MPI C/C++ that detects:
Deadlocks
MPI object leaks (e.g. communicators, requests, datatypes)
Functionally irrelevant barriers
Local assertion violations
MPI Send/Recv Type Mismatches
Offers rigorous coverage guarantees

Complete nondeterministic coverage for MPI (MPI_ANY_SOURCE)
Determines relevant interleavings, replaying as necessary
Examines communication / synchronization

behaviors
GEM
GEM-1
GEM - Overview
Front-end for In-situ Partial Order (ISP)
developed at University of Utah
Contributes push-button C/C++ MPI
verification and analysis to the
development cycle
Automatically instruments and runs user
code, displaying post verification results
Variety of views & tools to facilitate
debugging and MPI runtime
understanding
(Image courtesy of Steve Parker, U of Utah)
GEM
GEM-2
GEM Views & Tools

Analyzer View
Highlights bugs, and facilitates
post-verification review / debugging
GEM
Browser View
Groups and localizes MPI
problems. Maps errors to source
code in Eclipse editor
GEM-3
GEM Views & Tools (cont.)

Happens-Before Viewer
Shows required orderings and communication matches
(currently an external tool not supported in remote and
synchronized projects)
GEM
GEM-4
Plugins for GEM

GEM can be extended to import and analyze
MPI projects from the popular MPI
programming book:
Parallel Programming with MPI
by Peter Pacheco
Pacheco plugin was developed at University of Utah
(not part of PTP) with full permission by the books
author
An excellent way to learn MPI using PTP/GEM
Update Site: http://www.cs.utah.edu/formal_verification/Pacheco/
Prerequisite: PTP 6.0 with GEM installed
GEM
GEM-5
Pacheco Plugin
Ties in to GEM toolbar button
Provides a New
Eclipse View with
programming
examples from book
Automatically
import
examples into
workspace as
Eclipse C
projects
Build, work with and do

analysis on any of these
example projects using PTP
and GEM
GEM
GEM-6
GEM PTP Installation

This tutorial assumes that the GEM plugin for PTP is
installed they are not included by default in the
Eclipse for Parallel Application Developers package
GEM should already be installed for the tutorial, but the
installation section shows how to install GEM from the
PTP update site be sure GEM was selected
To confirm:
Help>Install New Software
Select the link: What is
already installed at the bottom
of the dialog
You should see the GEM there
GEM
GEM-7
GEM
Hands-on Section
GEM
GEM-8
GEM Hands-on (0)

Checkout GEM Project
(1) Check out GEM project gem-demo
from CVS repo. This is the same repository
as the shallow project.
1
(2) Check out using New Project Wizard
Create a new
Synchronized C Project
(3) Name the project:
2
GEM
gem-demo
Empty Makefile Project

Linux GCC toolchain for
both remote and local
GEM-9
GEM Hands-on (1)

Configure GEM Preferences
For the tutorial, you will only
need to set:
Remote ISP Paths
WindowPreferencesParallel ToolsGEM
Use the following for all remote

paths (ignore local):
/home/humphrey/isp/bin
Leave everything else at defaults
Click Apply and OK
GEM-10
GEM
GEM Hands-on (2)

Build GEM Project
Right click on gem-demo
Select Build Project
NOTE: The build automatically works here

because the GEM compiler wrapper
path is in the Makefile for the gemdemo project
GEM
Instrumented executable
(.gem extension) is visible
after build (output in console)
Force a project sync if this is
not visible
GEM-11
GEM Hands-on (3)

Set Number of Processes
Locate the trident
Icon on the Eclipse toolbar
From pull-down menu, set number of processes to 2
GEM
GEM-12
GEM Hands-on (4)

Locate file the profiled binary
MPI_MatrixMultiply.gem in the Project Explorer view
Right click on:
MPI_MatrixMultiply.gem
Select:
GEM -> Formally Verify Profiled MPI Program
GEM
Finally, wait for analysis. This may take

several seconds and you will see output in the
GEM Console View
GEM-13
GEM Hands-on (5)

Notice that three new Eclipse views have opened:
See next slide if your views are not positioned correctly
In the GEM Analyzer View (in focus by default),

notice there was a deadlock detected. No subsequent
errors or warning will be flagged until this is fixed
We can localize and fix this issue using:

GEM Analyzer View or the GEM Browser View
In this example, we will use the Analyzer View and the transition
navigation buttons
GEM
GEM-14
* FIX GEM VIEWS *

(NOTE: you may not need to do this)
Should look
like this now
Simply drag GEM views to position them

underneath the Eclipse Editor
GEM
GEM-15
GEM Hands-on (6)

Double Click on the Gem Analyzer View tab
This makes the view fill the workbench window
Fix the deadlock using the GEM Analyzer View

The GEM Analyzer View
should look similar to
this figure
MPI_MatrixMultiply.c
is open in both code
view windows. This is
where we will trace
execution as and MPI
calls (P2P and collective
matches) can be
examined as they
happened atGEM-16
runtime
GEM
GEM Hands-on (7)

Under Step Order for MPI Calls, select Internal
Issue Order. This is the order in which GEM issues
the intercepted MPI calls to the MPI runtime
Using the Transition Group, we will step through the
single interleaving discovered by GEM using the
navigation buttons.
First Transition
Focus on a specific rank
Previous Transition
Last Transition
Next Transition
GEM
GEM-17
GEM Hands-on (8)

Using navigation buttons:
Navigate to last transition
using last transition button
Then single step backward to
transition 25/26 using
previous transition button
Looking at 24/25, we see
its the last call to actually
complete before deadlocking,
so 25/26 is the problem
GEM
We are essentially looking at calls as issued to the MPI

runtime and reverse debugging to point of deadlock
GEM-18
GEM Hands-on (9)

Double click on the
highlighted recv
(25/26).
This takes you to line
in the Eclipse editor
Notice the comment:
this loop creates an
extra recv that will
never have a matching
send
Fix as suggested in the
comments
GEM
GEM-19
10
GEM Hands-on (10)

Rebuild the gem-demo project
Right click on:
MPI_MatrixMultiply.gem
Select:
GEM -> Formally Verify Profiled MPI Program
GEM
Finally, wait for analysis. This may take

several seconds and you will see output in the
GEM Console View
GEM-20
GEM Hands-on (11)

Notice again, the three GEM views:
GEM Analyzer, GEM Browser, GEM Console
In the GEM Analyzer View (in focus by default),

notice there were no MPI errors, e.g. deadlock,
assertion violation, but warnings were issued
Examine these warnings in the GEM Browser View

GEM
GEM-21
11
GEM Hands-on (12)

Click on the tab for the GEM Browser View
Notice GEM has found two types of warnings:

Functionally Irrelevant Barriers (unnecessary synchronization)
Resource Leaks (allocated MPI data types and communicators not freed)
GEM maps these warnings (and errors) to the

offending line of source code within the Eclipse editor
GEM
GEM-22
GEM Hands-on (13)

Click on Irrelevant Barriers tab
Expand the Interleaving 1 tree
Click on the FIB line
Notice you are taken to the
corresponding line in the
Eclipse Editor
This MPI_Barrier() call is
functionally irrelevant and
can be safely removed without
changing program behavior
Well investigate this further in
the exercise section at the
end of this section
GEM
GEM-23
12
GEM Hands-on (14)
NOTE
Fixing these warnings is left as an exercise
at the end of this section
GEM
GEM-24
GEM Hands-on (15)

Briefly examine the GEM help plugin
GEM Help also walks through the Managed-Build, PI-C
example created by the new MPI project wizard
Help -> Help Contents -> PTP -> GEM
GEM
GEM-25
13
Reference Slides
NOTE: The following slides are not part of the
presentation or hands-on section
They are meant to be used as further reference and
to provide more detailed information on:
GEM setup, configuration and preference pages
Using GEM views
Help contribution
Troubleshooting
GEM Success stories
GEM
GEM-26
ISP Installation
ISP itself must be installed prior to using GEM
Download ISP at http://www.cs.utah.edu/fv/ISP
Make sure libtool, automake and autoconf are installed.
Just untar isp-0.3.1.tar.gz into a tmp directory:
Configure and install
./configure prefix=/my/preferred/install/location
make
make install
This installs binaries and necessary scripts
GEM
GEM-27
14
GEM Preferences
Set preferences for GEM and its underlying
verification tool, ISP
GEM
GEM-28
GEM Analyzer View

Reports program errors, and runtime statistics
Debug-style source code stepping of interleavings
Point-to-point / Collective Operation matches
Internal Issue Order / Program Order views
Rank Lock feature focus on a particular process
Also controls:
Call Browser
Happens Before Viewer launch
Re-launching of GEM
GEM
GEM-29
15
GEM Browser View

Tabbed browsing for each type of MPI error/warning
Each error/warning mapped to offending line of
source code in Eclipse editor
One click to visit the Eclipse editor, to examine:
Calls involved in deadlock
Irrelevant barriers
MPI Object Leaks sites
MPI type mismatches
Local Assertion Violations
GEM
GEM-30
GEM Help Plugin

Extensive how-to sections, graphical aids and
trouble shooting section
GEM
GEM-31
16
GEM/ISP Success Stories

Umpire Tests
http://www.cs.utah.edu/fv/ISP-Tests
Documents bugs missed by tests, caught by ISP
MADRE (EuroPVM/MPI 2007)

Previously documented deadlock detected
N-Body Simulation Code

Previously unknown resource leak caught during
EuroPVM/MPI 2009 tutorial !
Large Case Studies

ParMETIS, MPI-BLAST, IRS (Sequoia Benchmark), and a few
SPEC-MPI benchmarks could be handled
Full Tutorial including LiveDVD ISO available

Visit http://www.cs.utah.edu/fv/GEM
GEM
GEM-32
Exercise (1) Fix MPI Warnings

1. Comment out the MPI_Barrier call on line 152
of MPI_MatrixMultiply.c
2. Uncomment lines 155 & 156 of the same
source file. These last two lines are the
corresponding free for the MPI
communicator that was created and also the
MPI datatype that was committed
3. Build the GEM project again to incorporate
these changes into the profiled executable
4. Re-run GEM and check that there are in fact
no errors or warnings
GEM
GEM-33
17
Exercise (2) Multiple Interleavings

1. Re-run GEM on the gem-demo project using
3 processes
2. How many Interleavings does GEM report?
3. Use the Interleaving navigation buttons to
explore this. You can reference GEM help for
the documentation on Interleaving navigation
buttons, or simply click the help icon in the
GEM Analyzer View to quickly navigate to
specific help with the GEM Analyzer View
GEM
GEM-34
18
Gcov and gprof support in linux tools

Objective
Learn how to use Eclipse-based interfaces to GNU tools
Gcov and Gprof
Contents
Build with -pg for gprof profiling
Build with -ftest-coverage fprofile-arcs for gcov
Run gcov to determine code coverage which parts of
your program are logically getting exercised
Run gprof to determined which parts of your program
are taking most of the execution time
Linux-0
Linux Tools
Linux Tools
http://eclipse.org/linuxtools
What is Linux Tools?

http://eclipse.org/linuxtoo
ls/
Builds on CDT for C/C++
Integrates popular native
development tools such as
Valgrind, OProfile, RPM,
SystemTap, GCov, GProf,
LTTng, etc. into Eclipse
Linux Tools
Linux-1
Linux Tools - Installation

Some of the Linux Tools
are included with Eclipse
for Parallel Application
Developers package
Everything you need for
this tutorial is in the
package
To install manually:
Help > Install New Software

In Work With: Select Juno update site
Under Linux Tools, Select the tools
you want or just select all of them
Some cannot be installed on all
non-Linux platforms
Click Next> and continue to end of
installation and restart Eclipse when
prompted
Linux-2
Linux Tools
Linux Tools - usage

With a synchronized project, you only need linuxtools
available on the remote system. (Even the Windows
client can view the gprof and gcov output files.)
Compiler flags
-pg to profile with gprof for the GNU compilers
-ftest-coverage -fprofile-arcs for gcov support
Its ok to use both at the same time at low optimization settings
Re-run the application

With synchronized projects, remember to re-sync to
retrieve the resultant files
gprof -s shallow gmon_shallow.* : creates a
summary profile (gmon.sum) from MPI programs with a
profile per rank
Linux Tools
Linux-3
Linux Tools click to view

Double-click gmon.* for gprof view
Double-click *.gcno or *.gcda for gcov view
Linux-4
Linux Tools
Linux Tools click to view

Double-click gmon.* for gprof view
Double-click *.gcno or *.gcda for gcov view,
It will ask for binary file location
Coverage Result: for Windows, select src file only (do not select the whole
binary file in the radio button of the dialog box)
Windows only.
Mac/Linux can show
coverage for whole
Windows
file
only
Linux Tools
Linux-5
Opening a profile with gprof viewer

Note: since weve changed filename from gmon.out to gmon_shallow.xxx
we will force the gprof editor to be invoked for the files.
Use Right mouse > Open With > Other and choose Gprof Editor
Linux-6
Linux Tools
Gprof tab
Double-click on gmon.out file to open
gprof viewer
Linux Tools
Linux-7
Run code, inspect gcov display

Double-click on a source file in gcov view to see
code coverage highlighted in source file
Linux Tools
Linux-8
Gcov with a production code, unexecuted region
Linux Tools
Linux-9
gprof with shallow project, MPI

Add compiler flags to Makefile
The Makefile CFLAGS and FFLAGS are modified as shown to

support profiling and coverage at the same time.
We have created the Makefile so you should just be able to
uncomment these lines.
Linux-10
Linux Tools
gprof with shallow project, MPI (2)

Modify Run Configuration
Run > Run Configurations to modify existing Run Configuration
Make this the fully qualified path+prefix

for gmon output. E.g.
/home/userid/shallow/gmon_shallow
(Otherwise they end up in a scratch dir)
Setup the MPI run configuration with the Environment variable

GMON_OUT_PREFIX defined with a /full/path/name for your
individual MPI rank gmon outputs. By default gmon.out is used but
MPI doesn't do that well and you end up with a profile that's missing
most of the information, so by using GMON_OUT_PREFIX, each MPI
rank adds its process id to its gmon output filename.
Linux Tools
Linux-11
gprof with shallow project, MPI (3)

Run from Run Configuration dialog
See build results in
Console
See new
files in Project Explorer
(You may need to
force a Sync)
Linux-12
Linux Tools
gprof with shallow project, 1 rank

Open gmon file with gprof viewer
Double-click on gmon.out file
-or- since gmon_shallow.xxx has non-standard file types .
Right click on gmon_shallow.xxx file and select
Rightmouse >Open With Other and select
Gprof Editor
Linux Tools
Linux-13
gprof with shallow project, 1 rank (2)

View gmon data with gprof viewer
It's interesting to
compare the summary
gmon output to that
from one of the ranks.
This view shows a
gmon.out file (you have
a gmon_shallow.xxx
file) from a single rank.
Linux Tools
Linux-14
Gprof with shallow project, summary

Aggregate the gmon output invoke from a terminal:
gprof -s shallow gmon_shallow.*
This creates a gmon.sum file
Force a sync to
see the file in
Project Explorer
Double-click to
open the gmon.sum
File with the
gprof viewer
Linux Tools
Linux-15
Gprof viewer does not currently

work well on Windows
Windows: gprof with
shallow project,
summary, use a
terminal window to
create text file
a.Invoke cmd line gprof
b.Sync to see file
c.Double-click to view
txt file
The linuxtools team
knows about the issue
with Juno and theyre
working on it.
Linux-16
Linux Tools
Gcov with shallow project

The gcov view is simlar to the gprof view but keep in mind that you're
looking at code coverage and not necessarily performance or timing
information (though there is a relationship...code not executed is
performing quite well ! ). Also note that multiple executions will
accumulate values in the gcov output files until they are removed or
truncated to zero-length (2nd run to demonstrate this).
Double-click
on any of the
*.gcda or *.gcno
to open this
gcov viewer
Linux Tools
Linux-17
Gcov with shallow project,

integration with CDT editor
Selecting (double click) a source code line from either the gcov or
gprof view and you'll see the file and routine highlighted in the
editor. Also notice the support for the .f90 file and its routines.
Linux-18
Linux Tools
Exercise
Follow directions in previous slides to
1. Add the compiler flags to Makefile
2. Modify run configuration as described (add gmon
prefix), and Run
3. View gmon and gcov files with gprof and gcov
viewers
Linux Tools
Linux-19
10
Optional Exercise
1) Run the shallow application with gcov compiler flags enabled.
a) Re-sync with Sync Active Now under Synchronization
b) View the tstep.gcno file and note the count, then repeat 1)a-b ,
have the counts changed?
2) Compare the tstep.f90 loops at lines 61, 70, 80 in the gprof and
gcov displays .
a) Change the Makefile to use O3 with FFLAGS and clean/rebuild/rerun
b) gprof s shallow gmon_shallow.273* [your most recent gmon_
files from the run you just finished ]
c) Re-sync the project
d) Does the gprof view of gmon.sum still exactly match up with the
gcov display? If not, what happened to the missing loop(s)?
Linux Tools
Linux-20
11
WRF & Eclipse

Objective
To learn how to work with the Weather Research and
Forecasting (WRF) code with Eclipse
Contents
Import WRF from local directory and make into
Checkout WRF from CVS repository, and make into
Interactive configure script execution
Driving makefile from Eclipse
Installation
Install-0
WRF Scenarios
Case A: User downloads tarball from WRF
download site
Case B: User checks out WRF from source
repository
Quirks
WRF uses a user-interactive configure script to get
things going
But, can drive make after configure script is initially
run
WRF
WRF-1
Things to watch for

Beware of helpful archive programs deciding
what is ascii, binary when extracting WRF
from its archive
Especially on windows
Execute bits do not seem to be set on scripts

Trying to understand the source of this issue
One scenario not shown (but very possible) is

to move the archive to the remote machine,
extract, and then synchronize the source from
the remote machine
Binary filters for synchronization could be very
important
WRF
WRF-2
Case A: WRF on local filesystem

Assuming you have
the source download
unpacked on your
local filesystem
Create new, empty
project
File>New>C Project
Makefile project,
empty project
Linux GCC
Project name
Finish
Installation
Install-3
Import WRF
Import WRF from
local filesystem
Right click on project
name, Import
General, Filesystem
Installation
Install-4
Filesystem Browser
Select Browse to
look at your local
filesystem
Navigate to source
directory
Installation
Install-5
Select source directory

Selecting directory
automatically selects
entire contents of
directory
Installation
Install-6
Add Fortran Flavor to project

Fortran projects are
derivatives of C/C++
projects
Can add Fortran
Flavor easily
Right click on project,
select Convert to
Fortran Project
Installation
Install-7
Convert to a synchronized
project
name, New>Other
Installation
Install-8
Select conversion wizard

Open Remote, then
Convert C/C++ or
Fortran Project to a
Synchronized
Project
Installation
Install-9
Converting to synchronized
project
Can only convert one
project at a time
New project is eligible
Select open
connection to
yellowstone
Destination directory
should autofill
Select Finish
Installation
Install-10
Case A complete
We have successfully imported source from
our filesystem, and pushed it to yellowstone
Next, well try checking out the code from CVS
WRF
WRF-11
Case B: Checking WRF out from

CVS
Notes
I checked WRF into CVS from Eclipse
If you check in WRF in from a

synchronized project, cannot remake
the checked out code into a synchronized
project
Hence, the code in the repository is not from a
But it is an Eclipse project, which

changes things a bit from the earlier
tutorial exercises
WRF
WRF-12
Back to CVS repository exploring

Change to the CVS Repository Exploring
Perspective
Using previous pserver connection, Open
Head, select WRF341_2
WRF
WRF-13
Check out as
Right click on
WRF341_2, select
Check out as
Note that since this
project is already an
Eclipse project, you
can only just check
out the project
Can rename on the
way (change project
name)
WRF
WRF-14
Convert to synchronized project

File>New>Other>
Remote, Convert
C/C++ or Fortran
Project to a
Synchronized
Project
Installation
Install-15
Interactive Configure
Switch to the
Remote System
Explorer perspective
Open SSH Terminal
to yellowstone
Ptp-03-01-shell
Dont enter
password
Yubikey...
WRF
WRF-16
Check permission of configure

Cd to WRF directory
on yellowstone
Chmod if necessary:
Run configure,
answering questions
appropriately
After configure, you
will have a Makefile
that you can
configure Eclipse to
drive
WRF
WRF-17
Synchronization Filtering
Git (used in
synchronized
projects) does not
like large, binary
files
Suggest to establish
filters on the project,
to prevent
performance issues
Right click on
project, Syncronize,
Filter
WRF
WRF-18
Filters using java regex
WRF
WRF-19
10
Java Regex reference

If not familiar with Java regex, this helped
me:
http://www.mkyong.com/regularexpressions/10-java-regular-expressionexamples-you-should-know/
WRF
WRF-20
Exercise
Create a WRF synchronized project
Set up some synchronization filters for your
synchonized project
Run configure script
Make WRF from Eclipse
Make run configuration for WRF
WRF
WRF-21
11
Sharing source code via CVS

Team, Share Project
Choose appropriate
repository
Installation
Install-22
Select appropriate repository

Select repository
Allow project name
to be module name
Installation
Install-23
12
Share resources
And launch the
commit wizard
Installation
Install-24
File types
Note that can
classify unknown file
types (and make
persistent)
Installation
Install-25
13
Add commit comment

Commit comment
Finish, and the
commit is done
Installation
Install-26
14
Tutorial Wrap-up
Objective
How to find more information on PTP
Learn about other tools related to PTP
See PTP upcoming features
Contents
Links to other tools, including performance tools
Planned features for new versions of PTP
Additional documentation
How to get involved
Tutorial Wrap Up
WrapUp-0
Useful Eclipse Tools

Linux Tools (autotools, valgrind, Oprofile, Gprof)
http://eclipse.org/linuxtools (part of Parallel package)
Python
http://pydev.org
Ruby
http://www.aptana.com/products/radrails
Perl
http://www.epic-ide.org
VI bindings
Vrapper (open source) - http://vrapper.sourceforge.net
viPlugin (commercial) - http://www.viplugin.com
Tutorial Wrap Up
WrapUp-1
Online Information
Information about PTP
PTP online help
http://help.eclipse.org
Main web site for downloads, documentation, etc.
http://eclipse.org/ptp
Wiki for designs, planning, meetings, etc.
http://wiki.eclipse.org/PTP
Information about Photran

Main web site for downloads, documentation, etc.
http://eclipse.org/photran
Tutorial Wrap Up
WrapUp-2
Mailing Lists
User Mailing Lists
PTP
http://dev.eclipse.org/mailman/listinfo/ptp-user
Photran
http://dev.eclipse.org/mailman/listinfo/photran
Major announcements (new releases, etc.) - low volume

http://dev.eclipse.org/mailman/listinfo/ptp-announce
Developer Mailing Lists

Developer discussions - higher volume
http://dev.eclipse.org/mailman/listinfo/ptp-dev
Tutorial Wrap Up
WrapUp-3
Getting Involved
See http://eclipse.org/ptp
Read the developer documentation on the wiki
http://wiki.eclipse.org/PTP
Join the mailing lists

Attend the monthly developer meetings
Conf Call Monthly: Second Tuesday, 1:00 pm ET

Details on the PTP wiki
Attend the monthly user meetings
Teleconf Monthly: 4th Wednesday, 1:00 pm ET

Details on the PTP wiki
Tutorial Wrap Up
WrapUp-4
PTP Tutorial Wrap-Up

PTP Tutorial @ XSEDE13
July 22, 2013; San Diego, CA
https://www.xsede.org/web/xsede13
Please complete feedback forms

Our paper feedback form (last 2 pages of handout)
Your feedback is valuable!

Thanks for attending
We hope you found it useful
Tutorial Wrap Up
WrapUp-5
SEA2013: April 4-5, 2013

A Unified Environment for the Development and
Tutorial Feedback
Performance Tuning of Parallel Scientific Applications
Thank you for attending our tutorial/workshop. As a part of an on-going effort to improve the
utility and usability of the tools we are developing, we are asking attendees to answer the
following questions. Note that all answers are anonymous. Comments are welcome anywhere.
1. Eclipse - how useful does Eclipse in general seem to you? (CIRCLE ONE)
1
2
3
4
5
very useful
Neutral
very useless
2. PTP: How useful does the functionality represented by this tool seem to you?
1
2
3
4
5
very useful
Neutral
very useless
Would you expect to increase your productivity by using this tool? If so, how much of an
increase in productivity do you think you may achieve by using this? Why?
______________________________________________________________________________
3. Usability: How usable do you think the tools are with their current interface?
1
2
3
4
5
very usable
Neutral
very unusable
Was there anything in particular that you found confusing or counterintuitive? If so, what?
______________________________________________________________________________
Do you have any suggestions for improving the user interface or additional functionality?
Please describe:
______________________________________________________________________________
4. Other tools?
What other tools would you like to see developed that would have a large impact on your own
productivity?
______________________________________________________________________________
What other tools would you like to see developed that would have a large impact on the
performance of the applications you work on?
______________________________________________________________________________
5. Tutorial presentation
How useful was the content of the workshop to your current position?
1
2
3
4
very useful
neutral
How well presented was the information?
1
2
3
excellent
good
satisfactory
How well did the instructors handle questions?
1
2
3
excellent
good
satisfactory
5
very useless
4
not so good
5
unacceptable
4
not so good
5
unacceptable
SEA2013: April 4-5, 2013

A Unified Environment for the Development and
Tutorial Feedback
Performance Tuning of Parallel Scientific Applications
Is there other material you would have liked to have had presented? If so, what?
______________________________________________________________________________
Is there material you think should be deleted? If so, what?
______________________________________________________________________________
6. Your Background:
How many years experience do you have in the IT industry? __________ In HPC? ___________
List languages in which you have written significant programs: ___________________________
Which is predominant currently? Why?
______________________________________________________________________________
Do you currently use an IDE (Integrated Development Environment, e.g. Eclipse)? If not, why?
If youve used Eclipse in the past, what has it helped you with? Has it helped you accomplish any
science results?
If you have not used Eclipse in the past, what do you see that it could help you with? Do you
think it may help you achieve any new science results faster, perhaps by helping make your
development more efficient?
______________________________________________________________________________
______________________________________________________________________________
What is your current job role?
______________________________________________________________________________
Can you describe the major application(s) you are working on now?
______________________________________________________________________________
Can you describe what you see as the major bottlenecks to increased productivity where you
work?
______________________________________________________________________________
______________________________________________________________________________
Are there any other relevant comments you want to share?
______________________________________________________________________________
(Optional) Name: _____________________________________Email:____________________
Thank you for your feedback!

SEA Tutorial Complete

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PTPCheatsheet

A Unified Environment for the

Wyatt Spear, U. Oregon

Galen Arnold, NCSA

April 4-5, 2013

1. Eclipse and PTP

Installation of Eclipse and PTP

2. Introduction & Overview

Eclipse architecture & organization overview

3. Developing with Eclipse

Eclipse basics; Creating a new project from CVS;

3. Developing with Eclipse

Continue from before the break

Debugging an MPI program

Debugging an MPI program

5a. Performance Tuning &

1. TAU (Tuning and Analysis Utilities)

5b. Performance Tuning &

2. Other tool integration with PTP

6. Developing WRF with

Overview of how to work with WRF from Eclipse

6. Developing WRF with

Overview of how to work with WRF from Eclipse

7. Other Tools, Wrapup

Other Tools, website, mailing lists, future features

Bring your own

Bring your own

PTP Tutorial Slide Topics

Adding a remote shell in Eclipse

Eclipse Editor Features

Using SSH tunnelling

Building a Project on a remote target

Running an Application on remote target

Search and Refactoring: Advanced Features

NCSA/XSEDE Features: GSI Authentication, MyProxy Login, etc

Performance Tools introduction

Performance Tools TAU (Tuning and Analysis Utilities)

Performance Tools GEM (Graphical Explorer of MPI Programs)

Performance Tools Linuxtools gcov/gprof in Eclipse

Final Slides, Installation

Java: Eclipse requires Sun or IBM Java

For PTP, we recommend the all-in-one

We often call this the Parallel Package

2. If your machine is Linux or Mac OS X, untar

3. If your machine is Windows, unzip the file

Eclipse Welcome Page

Checking for PTP Updates

PTP maintains its own update site with the most

Updating PTP: SEA

Updating PTP: SEA (2)

Updating PTP (2)

Note: for our tutorial, this installs extra features youll

Updating PTP (3)

Dont restart Eclipse yet!

Updating PTP CDT fix

Updating PTP - restart

Updating Individual Features

Icons indicate: Grey plug: already installed

Note: if network is slow, consider unchecking:

Restart after Install

Help>About or Eclipse > About Eclipse

5. Install the CDT fix

Parallel Tools Platform (PTP)

Eclipse PTP Family of Tools